jbrowse-plugin-graphgenomeviewer 6.9.1 → 6.9.2

package/dist/chunks/RgfaTabixAdapter-KOIMYOR3.js

@@ -0,0 +1,4 @@
+import{a as ge,b as he,d as $,e as z}from"./chunk-BFBKRNH4.js";import{g as B}from"./chunk-OEU2V7TV.js";import"./chunk-6AWRYNB2.js";import"./chunk-KWAXLUPQ.js";import"./chunk-YBLNN5FU.js";import{c as Z,e as A,f as G}from"./chunk-7QEJLDYY.js";import{a as j}from"./chunk-J4OLMLS5.js";import{b as R}from"./chunk-FY3BTKY4.js";var M=R(ge(),1),F=R(j(),1),le=R(he(),1);function I(s){let t=s.split("	"),e=t.length>=8,n=e?5:0;return{anchored:e,segment:{refName:t[n],start:+t[n+1],end:+t[n+2],id:t[3],rank:+t[4],tags:t[e?8:5]??""}}}function U(s){let t=s.tags.split(" ").find(n=>n.startsWith("SM:Z:"));if(t===void 0)return;let e=t.slice(5).split(",").map(n=>n.trim()).filter(Boolean);return e.length>0?e:void 0}function D(s){return{id:s.slice(0,-1),strand:s.slice(-1)}}function W(s){let t=s.split("	"),e=D(t[3]),n=D(t[4]);return{source:e.id,sourceStrand:e.strand,target:n.id,targetStrand:n.strand,sourceSegment:{id:e.id,refName:t[5],start:+t[6],end:+t[7],rank:+t[8],tags:t[13]??""},targetSegment:{id:n.id,refName:t[9],start:+t[10],end:+t[11],rank:+t[12],tags:t[14]??""}}}function y(s){return`${s.source}${s.sourceStrand}${s.target}${s.targetStrand}`}function _(s,t,e){let n=i=>i.rank!==0||i.refName!==e.refName?0:i.end<=e.start?-1:i.start>=e.end?1:0,r=new Map(s),a=new Map;for(let i of t)if(s.has(i.source)||s.has(i.target)||n(i.sourceSegment)*n(i.targetSegment)===-1){a.set(y(i),i);for(let o of[i.sourceSegment,i.targetSegment])r.has(o.id)||r.set(o.id,o)}for(let i of t)r.has(i.source)&&r.has(i.target)&&a.set(y(i),i);return{segments:r,links:a}}function K(s,t,e){let n=r=>r.refName!==e.refName||r.end<=e.start||r.start>=e.end;return[...Q(s.filter(r=>r.rank>0),t,e.end-e.start),...Q(s.filter(r=>r.rank===0&&n(r)),new Set(s.map(r=>r.id)),0)]}function Q(s,t,e){let n=[...s].sort((a,i)=>L(a.refName,i.refName)||a.start-i.start),r=[];for(let a of n){let i=r.at(-1);i?.refName===a.refName&&a.start-i.end<=e?(i.needed||=a.start>i.end||t.has(a.id),i.end=Math.max(i.end,a.end)):r.push({refName:a.refName,start:a.start,end:a.end,needed:t.has(a.id)})}return r.filter(a=>a.needed).map(({refName:a,start:i,end:o})=>({refName:a,start:i,end:o}))}function V(s,t,e){let n=r=>t.has(r.id)||e.some(a=>a.refName===r.refName&&r.start>=a.start&&r.end<=a.end);return s.filter(r=>n(r.sourceSegment)&&n(r.targetSegment))}var ke=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function be(s){let{id:t,refName:e,start:n,end:r,rank:a,tags:i}=s,o=i.split(" ").filter(l=>ke.test(l)),f=o.length===0?"":`	${o.join("	")}`;return`S	${t}	*	LN:i:${r-n}	SN:Z:${e}	SO:i:${n}	SR:i:${a}${f}`}function Se(s){let{source:t,sourceStrand:e,target:n,targetStrand:r}=s;return`L	${t}	${e}	${n}	${r}	0M`}function L(s,t){return s<t?-1:s>t?1:0}function O(s,t){let e=[...s.values()].sort((r,a)=>L(r.refName,a.refName)||r.start-a.start||L(r.id,a.id)),n=[...t.keys()].sort((r,a)=>L(r,a));return["H	VN:Z:1.0",...e.map(r=>be(r)),...n.map(r=>Se(t.get(r)))].join(`
+`)}var T=R(j(),1);function ee(s){let t=-1;for(let e=0;e<3;e++)t=s.indexOf("	",t+1);return s.slice(t+1,s.indexOf("	",t+1))}function te(s){let t=s.split("	",9);return{chunkStart:+t[1],name:t[3],fragStart:+t[4],hapOffset:+t[5],piece:+t[6],n:+t[7],enc:t[8]}}function J(s,t){let e=new RegExp(`(?:^|\\t)${t}:i:(\\d+)`).exec(s);return e?+e[1]:void 0}function ne(s){let t={references:[],haplotypes:[]};for(let e of s){let[n,r=""]=e.split("	");n==="#reference"?t.references.push(r):n==="#haplotype"?t.haplotypes.push(r):(t.chunk??=J(e,"chunk"),t.maxNode??=J(e,"maxnode"))}return t}function re(s,t){return s===void 0?1:Math.max(1,Math.ceil(s/t))}function P(s,t,e=1){return Math.max(0,(Math.floor(s/t)-e)*t)}function ae(s,t){return s===void 0||s.length===0?void 0:e=>A(e,t)||s.some(n=>A(e,n))}function we(s,t,e=new Int32Array(t),n=new Uint8Array(t),r=0){let a=0,i=r,o=0,f=!1;for(let l=0;l<=s.length;l++){let c=l<s.length?s.charCodeAt(l):44;if(c===44){let u=f?-o:o,d=u&1;n[i]=d,a+=(u-d)/2,e[i++]=a,o=0,f=!1}else c===45?f=!0:o=o*10+(c-48)}return{ids:e,rev:n}}function se(s){let t=new Map;for(let n of s){let r=`${n.name}	${n.fragStart}`,a=t.get(r);a?a.push(n):t.set(r,[n])}let e=[];for(let n of t.values()){n.sort((a,i)=>a.piece-i.piece);let r=0;for(let a=1;a<=n.length;a++)(a===n.length||n[a].piece!==n[a-1].piece+1)&&(e.push(xe(n.slice(r,a))),r=a)}return e}function xe(s){let t=s.reduce((a,i)=>a+i.n,0),e=new Int32Array(t),n=new Uint8Array(t),r=0;for(let a of s)we(a.enc,a.n,e,n,r),r+=a.n;return{name:s[0].name,hapOffset:s[0].hapOffset,ids:e,rev:n}}function oe(s,t){let e=o=>o?.onWindow===!0,n=new Set;for(let[o,f]of t)f.onWindow&&n.add(o);let r=[];for(let o of s){let{ids:f}=o,l=-1,c=-1;for(let u=0;u<f.length;u++)e(t.get(f[u]))&&(l<0&&(l=u),c=u);if(l>=0){for(let u=l;u<=c;u++)n.add(f[u]);r.push({run:o,first:l,last:c})}}let a=o=>{let f=t.get(o);return f===void 0?0:f.end-f.start},i=[];for(let{run:o,first:f,last:l}of r){let{ids:c,rev:u}=o,d=f,p=l;for(;d>0&&n.has(c[d-1]);)d--;for(;p<c.length-1&&n.has(c[p+1]);)p++;let h=o.hapOffset;for(let m=0;m<d;m++)h+=a(c[m]);let g=h;for(let m=d;m<=p;m++)g+=a(c[m]);i.push({name:o.name,hapStart:h,hapEnd:g,ids:c.subarray(d,p+1),rev:u.subarray(d,p+1)})}return{kept:n,fragments:i}}function Ne({name:s,hapStart:t,hapEnd:e,ids:n,rev:r}){let[a,i,...o]=s.split("#"),f=new Array(n.length);for(let l=0;l<n.length;l++)f[l]=(r[l]?"<":">")+n[l];return`W	${a}	${i}	${o.join("#")}	${t}	${e}	${f.join("")}`}function X(s,t,e){let n=-1;for(let r=0;r<t;r++)n=n===-1&&r>0?-1:s.indexOf("	",n+1),e[r]=n;return e}var v=class{constructor(t){this.window=t;this.nodes=new Map;this.links=[];this.t=[]}addNode(t){let e=X(t,8,this.t),n=+t.slice(e[2]+1,e[3]);if(!this.nodes.has(n)){let r=+t.slice(e[3]+1,e[4]),a=t.slice(e[4]+1,e[5]),i=+t.slice(e[5]+1,e[6]),o=+t.slice(e[6]+1,e[7]===-1?void 0:e[7]),{window:f}=this;this.nodes.set(n,{rank:r,refName:a,start:i,end:o,onWindow:r===0&&a===f.refName&&o>f.start-f.context&&i<f.end+f.context})}}addLink(t){let e=X(t,5,this.t);this.links.push(Y(t,e[2]+1,e[3]),Y(t,e[3]+1,e[4]===-1?t.length:e[4]))}format(t,e){let n=[];for(let o of t){let f=this.nodes.get(o);f&&n.push({...f,id:o})}n.sort((o,f)=>o.refName<f.refName?-1:o.refName>f.refName?1:o.start-f.start||o.id-f.id);let r=["H	VN:Z:1.1"];for(let{id:o,refName:f,start:l,end:c,rank:u}of n)r.push(`S	${o}	*	LN:i:${c-l}	SN:Z:${f}	SO:i:${l}	SR:i:${u}`);let a=new Set,i=[];for(let o=0;o<this.links.length;o+=2){let f=this.links[o],l=this.links[o+1],c=Math.floor(f/2),u=Math.floor(l/2);if(t.has(c)&&t.has(u)){let d=`L	${c}	${f%2?"-":"+"}	${u}	${l%2?"-":"+"}	0M`;a.has(d)||(a.add(d),i.push(d))}}return i.sort(),[...r,...i,...this.referenceFirst(e).map(Ne)].join(`
+`)}referenceFirst(t){let{refName:e}=this.window;return[...t].sort((n,r)=>+(r.name===e)-+(n.name===e)||(n.name<r.name?-1:n.name>r.name?1:n.hapStart-r.hapStart))}};function Y(s,t,e){return+s.slice(t,e-1)*2+(s.charCodeAt(e-1)===45?1:0)}function ie(s,t,e,n,r){let a=0,i=new Map,o=new Set;for(let p of s)a+=p.n,i.set(p.chunkStart,(i.get(p.chunkStart)??0)+p.n),o.add(p.name);if(a<=t)return;let f=e.end-e.start,l=0,c=0;for(let p of[...i.keys()].sort((h,g)=>h-g)){if(l+=i.get(p),l>t)break;c=Math.max(c,p+n-e.start)}let u=!r&&o.size>2&&2*a/o.size<=t,d=new B(t,f,Math.max(c,1));return d.message=c>0?`Zoom in to about ${(0,T.getBpDisplayStr)(c)}${u?", or choose fewer haplotypes,":""} to see the graph`:`Too many haplotype steps here to draw ${r?"these haplotypes":"every haplotype"} (${l.toLocaleString()} against walkStepBudget ${t.toLocaleString()}); choose fewer haplotypes`,d}async function fe(s,t,e,n){let r=await s(e.end);if(r<=t)return;let a=0,i;for(let l=Math.floor(e.start/n)*n;l<e.end;l+=n){let c=await s(l+1);if(i??=c,c>t)break;a=l+n-e.start}let o=e.end-e.start,f=new B(t,o,Math.max(a,1));return f.message=a>0?`Zoom in to about ${(0,T.getBpDisplayStr)(a)} to see the graph`:`Too much graph here to fetch (${q(i??r)} against walkByteBudget ${q(t)})`,f}var q=s=>`${(s/1e6).toFixed(1)} MB`;function ce(s){return s.filter(t=>t.rank>0)}function me(s,t,e){if(!Number.isFinite(t)||!Number.isFinite(e))throw new Error(`${s}:${t}-${e} is not a finite range to query the graph's index for`)}async function x(s,t,e,n,r){return me(t,e,n),s.getLines(t,e,n,r)}var ye=1e3,H=class extends M.BaseFeatureDataAdapter{constructor(e,n,r){super(e,n,r);this.walkHeader=(0,M.cachedSetup)({setup:async e=>{let n=this.fine.walks,r=ne(n?await n.getHeaderLines(e):[]),a=this.getConf("walkChunk"),i=r.chunk??a;return{...r,chunk:i,lookback:re(r.maxNode,i)}}});this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let n=$(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),r=this.getConf("walksLocation"),a=e.length===0&&(!("uri"in r)||r.uri!=="");return{segments:n,links:$(this,[...e,"linksLocation"],[...e,"linksIndex"]),walks:a?$(this,["walksLocation"],["walksIndex"]):void 0,refNames:new z(n,this)}}async walkQueryStart(e,n){let{chunk:r,lookback:a}=await this.walkHeader(n);return P(e,r,a)}async getHaplotypeNames(e={}){if(!this.fine.walks)return;let{haplotypes:n}=await this.walkHeader(e);return n.length>0?n:void 0}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,n={}){let{signal:r,statusCallback:a}=n;return(0,le.ObservableCreate)(async i=>{let o=await this.fine.refNames.resolve(e,n);if(o!==void 0){let f=this.fine.walks?await this.walkQueryStart(e.start,n):e.start;await(0,F.updateStatus)("Downloading segments",a,()=>x(this.fine.segments,o,f,e.end,{signal:r,lineCallback:l=>{let{segment:c,anchored:u}=I(l);if(u&&c.refName!==o)return;let d=U(c);i.next(new F.SimpleFeature({uniqueId:c.id,refName:e.refName,start:c.start,end:c.end,name:c.id,type:"segment",rank:c.rank,stableName:c.refName,...d&&{samples:d,sampleCount:d.length}}))}}))}i.complete()},r)}async getSubgraph(e,n={}){let{hops:r=0,signal:a,tier:i}=n,o=this.index(i),f=new Map,l=new Map,c=await o.refNames.resolve(e,{signal:a}),u=async(h,g,m)=>{let b=[];return await x(o.links,h,g,m,{signal:a,lineCallback:N=>{let S=W(N);l.set(y(S),S);for(let w of[S.sourceSegment,S.targetSegment])f.has(w.id)||(f.set(w.id,w),b.push(w))}}),b};if(c===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`);if(o.walks)return this.walkSubgraph(o,o.walks,c,e,n);let d={anchored:!1};if(await x(o.segments,c,e.start,e.end,{signal:a,lineCallback:h=>{let g=I(h);d.anchored||=g.anchored,f.set(g.segment.id,g.segment)}}),d.anchored){let h=[];await x(o.links,c,e.start,e.end,{signal:a,lineCallback:m=>{h.push(W(m))}});let g=_(f,h,{refName:c,start:e.start,end:e.end});return O(g.segments,g.links)}let p=ce(await u(c,e.start,e.end));for(let h=0;h<r;h++){let g=await Promise.all(p.map(m=>u(m.refName,m.start,m.end)));p=ce(g.flat())}if(r>0){let h=K([...f.values()],new Set(p.map(m=>m.id)),{refName:c,start:e.start,end:e.end}),g=[];await Promise.all(h.map(m=>x(o.links,m.refName,m.start,m.end,{signal:a,lineCallback:b=>{g.push(W(b))}})));for(let m of V(g,f,h)){l.set(y(m),m);for(let b of[m.sourceSegment,m.targetSegment])f.has(b.id)||f.set(b.id,b)}}return O(f,l)}async walkSubgraph(e,n,r,a,i){let{signal:o,haplotypes:f}=i,{chunk:l,lookback:c}=await this.walkHeader({signal:o}),u=this.getConf("walkStepBudget"),d=ae(f?.map(k=>G(this,k)),Z(r)),p=P(a.start,l,c),h=[n,e.segments,e.links],g=await fe(async k=>(me(r,p,k),(await Promise.all(h.map(C=>C.bytesForRegions([{refName:r,start:p,end:k}],{signal:o})))).reduce((C,pe)=>C+pe,0)),this.getConf("walkByteBudget"),a,l);if(g)throw g;let m=new AbortController,b=()=>{m.abort(o?.reason)};o?.addEventListener("abort",b,{once:!0});let N=[],S=new v({refName:r,start:a.start,end:a.end,context:ye}),w=(k,E)=>x(k,r,p,a.end,{signal:m.signal,lineCallback:E});try{await Promise.all([w(n,k=>{(d===void 0||d(ee(k)))&&N.push(te(k))}).then(()=>{let k=ie(N,u,a,l,d!==void 0);if(k)throw k}),w(e.segments,k=>{S.addNode(k)}),w(e.links,k=>{S.addLink(k)})])}catch(k){throw m.abort(),k}finally{o?.removeEventListener("abort",b)}let{kept:ue,fragments:de}=oe(se(N),S.nodes);return S.format(ue,de)}};export{H as default};
+//# sourceMappingURL=RgfaTabixAdapter-KOIMYOR3.js.map

package/dist/chunks/RgfaTabixAdapter-KOIMYOR3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts", "../../src/RgfaTabixAdapter/rgfaBed.ts", "../../src/RgfaTabixAdapter/walkRows.ts"],
+  "sourcesContent": ["import { panSNHaplotype, resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport {\n  BaseFeatureDataAdapter,\n  cachedSetup,\n} 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'\nimport {\n  WalkGraph,\n  byteBudgetError,\n  chunkQueryStart,\n  joinPieces,\n  lookbackChunks,\n  parseWalkRow,\n  stepBudgetError,\n  walkCut,\n  walkHeader,\n  walkNameFilter,\n  walkRowName,\n} from './walkRows.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { WalkRow } from './walkRows.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 { FileLocation, 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\n// tabix-js loops forever on a NaN end and reads nothing for a NaN start\n// (GMOD/tabix-js#157), so every query the adapter makes refuses a range that\n// is not finite first\nfunction checkRange(refName: string, start: number, end: number) {\n  if (!Number.isFinite(start) || !Number.isFinite(end)) {\n    throw new Error(\n      `${refName}:${start}-${end} is not a finite range to query the graph's index for`,\n    )\n  }\n}\n\nasync function getLines(\n  file: TabixIndexedFile,\n  refName: string,\n  start: number,\n  end: number,\n  opts: { signal?: AbortSignal; lineCallback: (line: string) => void },\n) {\n  checkRange(refName, start, end)\n  return file.getLines(refName, start, end, opts)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: TabixIndexedFile\n  refNames: PanSNRefNames\n}\n\n// How much graph a walk cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\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    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const hasWalks =\n      under.length === 0 &&\n      (!('uri' in walksLocation) || walksLocation.uri !== '')\n    return {\n      segments,\n      links: openTabixSlot(\n        this,\n        [...under, 'linksLocation'],\n        [...under, 'linksIndex'],\n      ),\n      walks: hasWalks\n        ? openTabixSlot(this, ['walksLocation'], ['walksIndex'])\n        : undefined,\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  // A walk-indexed graph's header: the chunk its rows are filed under, else\n  // the walkChunk slot, how many chunks before a window a cut reads, and the\n  // haplotypes it names\n  private walkHeader = cachedSetup({\n    setup: async opts => {\n      const walks = this.fine.walks\n      const header = walkHeader(walks ? await walks.getHeaderLines(opts) : [])\n      const slot: number = this.getConf('walkChunk')\n      const chunk = header.chunk ?? slot\n      return {\n        ...header,\n        chunk,\n        lookback: lookbackChunks(header.maxNode, chunk),\n      }\n    },\n  })\n\n  private async walkQueryStart(start: number, opts: BaseOptions) {\n    const { chunk, lookback } = await this.walkHeader(opts)\n    return chunkQueryStart(start, chunk, lookback)\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    if (!this.fine.walks) {\n      return undefined\n    }\n    const { haplotypes } = await this.walkHeader(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\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        // a walk-indexed node row names only its chunk's first base, and a\n        // node crossing in from a chunk before is filed there\n        const start = this.fine.walks\n          ? await this.walkQueryStart(query.start, opts)\n          : query.start\n        await updateStatus('Downloading segments', statusCallback, () =>\n          getLines(this.fine.segments, tabixRefName, 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 getLines(index.links, 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    if (index.walks) {\n      return this.walkSubgraph(index, index.walks, tabixRefName, region, opts)\n    }\n    const layout = { anchored: false }\n    await getLines(index.segments, 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 getLines(index.links, 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          getLines(index.links, 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 walk-indexed graph's cut: one read of each file over whole chunks, from\n  // the lookback chunks before the window to its end. The indexes first\n  // estimate the bytes those reads fetch, and a window past walkByteBudget\n  // reads no row. Only the walks `haplotypes` asks for, and the reference's,\n  // are decoded, and none is past walkStepBudget: the three reads go out\n  // together and a walk read over budget stops the other two.\n  private async walkSubgraph(\n    index: GraphIndex,\n    walks: TabixIndexedFile,\n    refName: string,\n    region: Region,\n    opts: SubgraphAdapterOptions,\n  ) {\n    const { signal, haplotypes } = opts\n    const { chunk, lookback } = await this.walkHeader({ signal })\n    const budget: number = this.getConf('walkStepBudget')\n    const keep = walkNameFilter(\n      haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n      panSNHaplotype(refName),\n    )\n    const from = chunkQueryStart(region.start, chunk, lookback)\n    const files = [walks, index.segments, index.links]\n    const tooLarge = await byteBudgetError(\n      async end => {\n        checkRange(refName, from, end)\n        const sizes = await Promise.all(\n          files.map(file =>\n            file.bytesForRegions([{ refName, start: from, end }], { signal }),\n          ),\n        )\n        return sizes.reduce((sum, bytes) => sum + bytes, 0)\n      },\n      this.getConf('walkByteBudget'),\n      region,\n      chunk,\n    )\n    if (tooLarge) {\n      throw tooLarge\n    }\n    const reads = new AbortController()\n    const stop = () => {\n      reads.abort(signal?.reason)\n    }\n    signal?.addEventListener('abort', stop, { once: true })\n    const rows: WalkRow[] = []\n    const graph = new WalkGraph({\n      refName,\n      start: region.start,\n      end: region.end,\n      context: WALK_CONTEXT,\n    })\n    const read = (\n      file: TabixIndexedFile,\n      lineCallback: (line: string) => void,\n    ) =>\n      getLines(file, refName, from, region.end, {\n        signal: reads.signal,\n        lineCallback,\n      })\n    try {\n      await Promise.all([\n        read(walks, line => {\n          if (keep === undefined || keep(walkRowName(line))) {\n            rows.push(parseWalkRow(line))\n          }\n        }).then(() => {\n          const error = stepBudgetError(\n            rows,\n            budget,\n            region,\n            chunk,\n            keep !== undefined,\n          )\n          if (error) {\n            throw error\n          }\n        }),\n        read(index.segments, line => {\n          graph.addNode(line)\n        }),\n        read(index.links, line => {\n          graph.addLink(line)\n        }),\n      ])\n    } catch (error) {\n      reads.abort()\n      throw error\n    } finally {\n      signal?.removeEventListener('abort', stop)\n    }\n    const { kept, fragments } = walkCut(joinPieces(rows), graph.nodes)\n    return graph.format(kept, fragments)\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. A span whose segments were all read and abut is skipped.\nexport function closingSpans(\n  held: RgfaSegment[],\n  unread: Set<string>,\n  window: StableSpan,\n) {\n  const outside = (segment: RgfaSegment) =>\n    segment.refName !== window.refName ||\n    segment.end <= window.start ||\n    segment.start >= window.end\n  return [\n    ...mergedSpans(\n      held.filter(segment => segment.rank > 0),\n      unread,\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      new Set(held.map(segment => segment.id)),\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  unread: Set<string>,\n  maxGap: number,\n) {\n  const sorted = [...segments].sort(\n    (a, b) => compare(a.refName, b.refName) || a.start - b.start,\n  )\n  const spans: (StableSpan & { needed: boolean })[] = []\n  for (const segment of sorted) {\n    const span = spans.at(-1)\n    if (\n      span?.refName === segment.refName &&\n      segment.start - span.end <= maxGap\n    ) {\n      span.needed ||= segment.start > span.end || unread.has(segment.id)\n      span.end = Math.max(span.end, segment.end)\n    } else {\n      spans.push({\n        refName: segment.refName,\n        start: segment.start,\n        end: segment.end,\n        needed: unread.has(segment.id),\n      })\n    }\n  }\n  return spans\n    .filter(span => span.needed)\n    .map(({ refName, start, end }): StableSpan => ({ refName, start, end }))\n}\n\n// The links a closing read keeps: each end is a segment the cut holds or one\n// lying inside a span. 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", "import { NodeLimitError } from '@jbrowse/bandage-core/gbzWindow'\nimport { panSNMatchesPrefix } from '@jbrowse/bandage-core/pansn'\nimport { getBpDisplayStr } from '@jbrowse/core/util'\n\n// A walk-indexed graph is three tabix files filed under fixed chunks of each\n// reference: walk rows, node rows and link rows. A row's first three columns\n// name its chunk, either as the whole chunk or as its first base.\n//\n//   walks: anchor cs ce sample#hap#contig fragStart hapOffset piece nsteps steps\n//   nodes: anchor cs ce id rank stableName start end [tags]\n//   links: anchor cs ce src+ tgt- [both endpoints' coordinates]\n//\n// Steps are node-id deltas with the orientation in the low bit,\n// comma-separated, the first of each row absolute. A haplotype path's piece in\n// one chunk is cut into rows of at most a fixed number of steps, and each row\n// takes the next piece index, so consecutive indices of one path join.\nexport interface WalkRow {\n  name: string\n  fragStart: number\n  hapOffset: number\n  piece: number\n  n: number\n  enc: string\n  chunkStart: number\n}\n\nexport interface WalkNode {\n  refName: string\n  start: number\n  end: number\n  rank: number\n  // on the reference inside the window plus the cut's context\n  onWindow: boolean\n}\n\nexport interface WalkWindow {\n  refName: string\n  start: number\n  end: number\n  context: number\n}\n\n// The name column, read without splitting the steps, so a row the cut does\n// not want costs a few indexOf calls\nexport function walkRowName(line: string) {\n  let at = -1\n  for (let k = 0; k < 3; k++) {\n    at = line.indexOf('\\t', at + 1)\n  }\n  return line.slice(at + 1, line.indexOf('\\t', at + 1))\n}\n\nexport function parseWalkRow(line: string): WalkRow {\n  const c = line.split('\\t', 9)\n  return {\n    chunkStart: +c[1]!,\n    name: c[3]!,\n    fragStart: +c[4]!,\n    hapOffset: +c[5]!,\n    piece: +c[6]!,\n    n: +c[7]!,\n    enc: c[8]!,\n  }\n}\n\nexport interface WalkHeader {\n  chunk?: number\n  maxNode?: number\n  references: string[]\n  haplotypes: string[]\n}\n\nfunction integerTag(line: string, tag: string) {\n  const match = new RegExp(`(?:^|\\\\t)${tag}:i:(\\\\d+)`).exec(line)\n  return match ? +match[1]! : undefined\n}\n\n/**\n * What a walk file's header states: its chunk size in a\n * `#walks\\tchunk:i:65536` line, from gfa-to-tabix 0.4.0 a\n * `#reference\\tGRCh38` line per reference sample and a\n * `#haplotype\\tHG002#1` line per other haplotype with rows, and from 0.5.0\n * the longest node in bp as `maxnode:i:1024` beside the chunk size\n */\nexport function walkHeader(lines: string[]): WalkHeader {\n  const header: WalkHeader = { references: [], haplotypes: [] }\n  for (const line of lines) {\n    const [key, value = ''] = line.split('\\t')\n    if (key === '#reference') {\n      header.references.push(value)\n    } else if (key === '#haplotype') {\n      header.haplotypes.push(value)\n    } else {\n      header.chunk ??= integerTag(line, 'chunk')\n      header.maxNode ??= integerTag(line, 'maxnode')\n    }\n  }\n  return header\n}\n\n/**\n * How many chunks before the window's own a cut reads. A node is filed under\n * the chunk holding its start, so a node `maxNode` bp long reaching into the\n * window starts at most ceil(maxNode / chunk) chunks back. At least one, since\n * the chunk before carries the detour a haplotype takes into the window's\n * first reference node; one when the header gives no `maxnode:i:`, which holds\n * for vg's graphs, chopped to nodes of at most 1,024 bp.\n */\nexport function lookbackChunks(maxNode: number | undefined, chunk: number) {\n  return maxNode === undefined ? 1 : Math.max(1, Math.ceil(maxNode / chunk))\n}\n\n// The first base a cut queries: the start of the chunk `lookback` chunks\n// before the one holding the window's start\nexport function chunkQueryStart(start: number, chunk: number, lookback = 1) {\n  return Math.max(0, (Math.floor(start / chunk) - lookback) * chunk)\n}\n\n// Which walks a cut decodes: the reference's, and those `wanted` names by\n// PanSN prefix at sample or haplotype depth; undefined decodes every one\nexport function walkNameFilter(\n  wanted: string[] | undefined,\n  referenceHaplotype: string | undefined,\n) {\n  return wanted === undefined || wanted.length === 0\n    ? undefined\n    : (name: string) =>\n        panSNMatchesPrefix(name, referenceHaplotype) ||\n        wanted.some(prefix => panSNMatchesPrefix(name, prefix))\n}\n\nexport function decodeSteps(\n  enc: string,\n  n: number,\n  ids = new Int32Array(n),\n  rev = new Uint8Array(n),\n  at = 0,\n) {\n  let prev = 0\n  let i = at\n  let v = 0\n  let neg = false\n  for (let p = 0; p <= enc.length; p++) {\n    const ch = p < enc.length ? enc.charCodeAt(p) : 44\n    if (ch === 44) {\n      const d = neg ? -v : v\n      const r = d & 1\n      rev[i] = r\n      prev += (d - r) / 2\n      ids[i++] = prev\n      v = 0\n      neg = false\n    } else if (ch === 45) {\n      neg = true\n    } else {\n      v = v * 10 + (ch - 48)\n    }\n  }\n  return { ids, rev }\n}\n\n// One stretch of a haplotype path: rows of consecutive piece index, decoded\nexport interface WalkRun {\n  name: string\n  hapOffset: number\n  ids: Int32Array\n  rev: Uint8Array\n}\n\nexport function joinPieces(rows: WalkRow[]) {\n  const byPath = new Map<string, WalkRow[]>()\n  for (const row of rows) {\n    const key = `${row.name}\\t${row.fragStart}`\n    const list = byPath.get(key)\n    if (list) {\n      list.push(row)\n    } else {\n      byPath.set(key, [row])\n    }\n  }\n  const runs: WalkRun[] = []\n  for (const pieces of byPath.values()) {\n    pieces.sort((a, b) => a.piece - b.piece)\n    let from = 0\n    for (let i = 1; i <= pieces.length; i++) {\n      if (\n        i === pieces.length ||\n        pieces[i]!.piece !== pieces[i - 1]!.piece + 1\n      ) {\n        runs.push(decodeRun(pieces.slice(from, i)))\n        from = i\n      }\n    }\n  }\n  return runs\n}\n\nfunction decodeRun(pieces: WalkRow[]): WalkRun {\n  const n = pieces.reduce((sum, p) => sum + p.n, 0)\n  const ids = new Int32Array(n)\n  const rev = new Uint8Array(n)\n  let at = 0\n  for (const p of pieces) {\n    decodeSteps(p.enc, p.n, ids, rev, at)\n    at += p.n\n  }\n  return { name: pieces[0]!.name, hapOffset: pieces[0]!.hapOffset, ids, rev }\n}\n\nexport interface WalkFragment {\n  name: string\n  hapStart: number\n  hapEnd: number\n  ids: Int32Array\n  rev: Uint8Array\n}\n\n/**\n * The cut a window draws from its walks: the reference inside the window plus\n * its context, and each run from its first to its last step on that stretch,\n * run on outward while the next step's node is already in the cut. Without\n * the run-on a haplotype whose alternate allele straddles the edge stopped\n * short of a node other walks had brought into the cut, and that node drew\n * without it. The run-on adds no node, so one pass is enough.\n */\nexport function walkCut(runs: WalkRun[], nodes: Map<number, WalkNode>) {\n  const onWindow = (node: WalkNode | undefined) => node?.onWindow === true\n  const kept = new Set<number>()\n  for (const [id, node] of nodes) {\n    if (node.onWindow) {\n      kept.add(id)\n    }\n  }\n  const spans: { run: WalkRun; first: number; last: number }[] = []\n  for (const run of runs) {\n    const { ids } = run\n    let first = -1\n    let last = -1\n    for (let i = 0; i < ids.length; i++) {\n      if (onWindow(nodes.get(ids[i]!))) {\n        if (first < 0) {\n          first = i\n        }\n        last = i\n      }\n    }\n    if (first >= 0) {\n      for (let i = first; i <= last; i++) {\n        kept.add(ids[i]!)\n      }\n      spans.push({ run, first, last })\n    }\n  }\n  const length = (id: number) => {\n    const node = nodes.get(id)\n    return node === undefined ? 0 : node.end - node.start\n  }\n  const fragments: WalkFragment[] = []\n  for (const { run, first: f, last: l } of spans) {\n    const { ids, rev } = run\n    let first = f\n    let last = l\n    while (first > 0 && kept.has(ids[first - 1]!)) {\n      first--\n    }\n    while (last < ids.length - 1 && kept.has(ids[last + 1]!)) {\n      last++\n    }\n    let hapStart = run.hapOffset\n    for (let i = 0; i < first; i++) {\n      hapStart += length(ids[i]!)\n    }\n    let hapEnd = hapStart\n    for (let i = first; i <= last; i++) {\n      hapEnd += length(ids[i]!)\n    }\n    fragments.push({\n      name: run.name,\n      hapStart,\n      hapEnd,\n      ids: ids.subarray(first, last + 1),\n      rev: rev.subarray(first, last + 1),\n    })\n  }\n  return { kept, fragments }\n}\n\nexport function formatWalk({ name, hapStart, hapEnd, ids, rev }: WalkFragment) {\n  const [sample, haplotype, ...contig] = name.split('#')\n  const steps = new Array<string>(ids.length)\n  for (let i = 0; i < ids.length; i++) {\n    steps[i] = (rev[i] ? '<' : '>') + ids[i]\n  }\n  return `W\\t${sample}\\t${haplotype}\\t${contig.join('#')}\\t${hapStart}\\t${hapEnd}\\t${steps.join('')}`\n}\n\n// The positions of a line's first `n` tabs, -1 past the last\nfunction tabs(line: string, n: number, out: number[]) {\n  let at = -1\n  for (let k = 0; k < n; k++) {\n    at = at === -1 && k > 0 ? -1 : line.indexOf('\\t', at + 1)\n    out[k] = at\n  }\n  return out\n}\n\n/**\n * The node and link rows a walk cut reads, parsed as they arrive, and the GFA\n * text of the cut they make with its walks. A node filed under two chunks\n * arrives twice and is read once; columns past a node row's eighth (LN:i:,\n * SQ:Z: and whatever follows) are not read at all.\n */\nexport class WalkGraph {\n  readonly nodes = new Map<number, WalkNode>()\n  private links: number[] = []\n  private readonly t: number[] = []\n\n  constructor(private window: WalkWindow) {}\n\n  addNode(line: string) {\n    const t = tabs(line, 8, this.t)\n    const id = +line.slice(t[2]! + 1, t[3])\n    if (!this.nodes.has(id)) {\n      const rank = +line.slice(t[3]! + 1, t[4])\n      const refName = line.slice(t[4]! + 1, t[5])\n      const start = +line.slice(t[5]! + 1, t[6])\n      const end = +line.slice(t[6]! + 1, t[7] === -1 ? undefined : t[7])\n      const { window } = this\n      this.nodes.set(id, {\n        rank,\n        refName,\n        start,\n        end,\n        onWindow:\n          rank === 0 &&\n          refName === window.refName &&\n          end > window.start - window.context &&\n          start < window.end + window.context,\n      })\n    }\n  }\n\n  // An endpoint is held as id * 2 + 1 when reversed\n  addLink(line: string) {\n    const t = tabs(line, 5, this.t)\n    this.links.push(\n      endpoint(line, t[2]! + 1, t[3]!),\n      endpoint(line, t[3]! + 1, t[4] === -1 ? line.length : t[4]!),\n    )\n  }\n\n  /**\n   * GFA text: S lines by reference position, then L lines, then a W line per\n   * fragment, the reference's first and the rest by name, the same bytes for\n   * the same rows\n   */\n  format(kept: Set<number>, fragments: WalkFragment[]) {\n    const held: (WalkNode & { id: number })[] = []\n    for (const id of kept) {\n      const node = this.nodes.get(id)\n      if (node) {\n        held.push({ ...node, id })\n      }\n    }\n    held.sort((x, y) =>\n      x.refName < y.refName\n        ? -1\n        : x.refName > y.refName\n          ? 1\n          : x.start - y.start || x.id - y.id,\n    )\n    const lines = ['H\\tVN:Z:1.1']\n    for (const { id, refName, start, end, rank } of held) {\n      lines.push(\n        `S\\t${id}\\t*\\tLN:i:${end - start}\\tSN:Z:${refName}\\tSO:i:${start}\\tSR:i:${rank}`,\n      )\n    }\n    const seen = new Set<string>()\n    const links: string[] = []\n    for (let i = 0; i < this.links.length; i += 2) {\n      const a = this.links[i]!\n      const b = this.links[i + 1]!\n      const source = Math.floor(a / 2)\n      const target = Math.floor(b / 2)\n      if (kept.has(source) && kept.has(target)) {\n        const line = `L\\t${source}\\t${a % 2 ? '-' : '+'}\\t${target}\\t${b % 2 ? '-' : '+'}\\t0M`\n        if (!seen.has(line)) {\n          seen.add(line)\n          links.push(line)\n        }\n      }\n    }\n    links.sort()\n    return [\n      ...lines,\n      ...links,\n      ...this.referenceFirst(fragments).map(formatWalk),\n    ].join('\\n')\n  }\n\n  // The view anchors on the first walk when no walk names the assembly, as\n  // gbz-base's cut has it; in file order that was whichever haplotype the\n  // chunk listed first, CHM13 on a GRCh38 window\n  private referenceFirst(fragments: WalkFragment[]) {\n    const { refName } = this.window\n    return [...fragments].sort(\n      (a, b) =>\n        Number(b.name === refName) - Number(a.name === refName) ||\n        (a.name < b.name ? -1 : a.name > b.name ? 1 : a.hapStart - b.hapStart),\n    )\n  }\n}\n\nfunction endpoint(line: string, from: number, to: number) {\n  return (\n    +line.slice(from, to - 1) * 2 + (line.charCodeAt(to - 1) === 45 ? 1 : 0)\n  )\n}\n\n/**\n * The zoom-in notice for a cut whose walk rows hold more steps than `budget`,\n * or undefined when they fit. A window reads whole chunks, those before it\n * included, so the span that fits is counted in chunks from the window's\n * start; when the chunks a window there always reads are over on their own,\n * no zoom fits and the notice asks for fewer haplotypes. A cut for every\n * haplotype is also offered fewer where the reference and one haplotype, at\n * the walks' average steps, would fit the whole window.\n */\nexport function stepBudgetError(\n  rows: WalkRow[],\n  budget: number,\n  window: { start: number; end: number },\n  chunk: number,\n  filtered: boolean,\n) {\n  let total = 0\n  const perChunk = new Map<number, number>()\n  const walks = new Set<string>()\n  for (const row of rows) {\n    total += row.n\n    perChunk.set(row.chunkStart, (perChunk.get(row.chunkStart) ?? 0) + row.n)\n    walks.add(row.name)\n  }\n  if (total <= budget) {\n    return undefined\n  }\n  const windowBp = window.end - window.start\n  let read = 0\n  let fitsBp = 0\n  for (const cs of [...perChunk.keys()].sort((a, b) => a - b)) {\n    read += perChunk.get(cs)!\n    if (read > budget) {\n      break\n    }\n    fitsBp = Math.max(fitsBp, cs + chunk - window.start)\n  }\n  const fewerFit =\n    !filtered && walks.size > 2 && (2 * total) / walks.size <= budget\n  const error = new NodeLimitError(budget, windowBp, Math.max(fitsBp, 1))\n  error.message =\n    fitsBp > 0\n      ? `Zoom in to about ${getBpDisplayStr(fitsBp)}${fewerFit ? ', or choose fewer haplotypes,' : ''} to see the graph`\n      : `Too many haplotype steps here to draw ${filtered ? 'these haplotypes' : 'every haplotype'} (${read.toLocaleString()} against walkStepBudget ${budget.toLocaleString()}); choose fewer haplotypes`\n  return error\n}\n\n/**\n * The zoom-in notice for a cut whose three files would fetch more than\n * `budget` compressed bytes, or undefined when they fit. `bytesTo(end)` is the\n * indexes' estimate for a read from the window's first query base to `end`;\n * the span that fits grows a chunk at a time from the chunk holding the\n * window's start, and when that chunk and those before it are over on their\n * own, no zoom fits.\n */\nexport async function byteBudgetError(\n  bytesTo: (end: number) => Promise<number>,\n  budget: number,\n  window: { start: number; end: number },\n  chunk: number,\n) {\n  const bytes = await bytesTo(window.end)\n  if (bytes <= budget) {\n    return undefined\n  }\n  let fitsBp = 0\n  let least: number | undefined\n  for (\n    let cs = Math.floor(window.start / chunk) * chunk;\n    cs < window.end;\n    cs += chunk\n  ) {\n    const read = await bytesTo(cs + 1)\n    least ??= read\n    if (read > budget) {\n      break\n    }\n    fitsBp = cs + chunk - window.start\n  }\n  const windowBp = window.end - window.start\n  const error = new NodeLimitError(budget, windowBp, Math.max(fitsBp, 1))\n  error.message =\n    fitsBp > 0\n      ? `Zoom in to about ${getBpDisplayStr(fitsBp)} to see the graph`\n      : `Too much graph here to fetch (${megabytes(least ?? bytes)} against walkByteBudget ${megabytes(budget)})`\n  return error\n}\n\nconst megabytes = (bytes: number) => `${(bytes / 1e6).toFixed(1)} MB`\n"],
+  "mappings": "iUACA,IAAAA,EAGO,UACPC,EAA4C,SAC5CC,GAAiC,UCiC1B,SAASC,EAAgBC,EAAc,CAC5C,IAAMC,EAAOD,EAAK,MAAM,GAAI,EACtBE,EAAWD,EAAK,QAAU,EAC1BE,EAAMD,EAAW,EAAI,EAC3B,MAAO,CACL,SAAAA,EACA,QAAS,CACP,QAASD,EAAKE,CAAG,EACjB,MAAO,CAACF,EAAKE,EAAM,CAAC,EACpB,IAAK,CAACF,EAAKE,EAAM,CAAC,EAClB,GAAIF,EAAK,CAAC,EACV,KAAM,CAACA,EAAK,CAAC,EACb,KAAMA,EAAKC,EAAW,EAAI,CAAC,GAAK,EAClC,CACF,CACF,CAiBO,SAASE,EAAeC,EAAsB,CACnD,IAAMC,EAAMD,EAAQ,KAAK,MAAM,GAAG,EAAE,KAAKE,GAAKA,EAAE,WAAW,OAAO,CAAC,EACnE,GAAID,IAAQ,OACV,OAEF,IAAME,EAAUF,EACb,MAAM,CAAc,EACpB,MAAM,GAAG,EACT,IAAIG,GAAKA,EAAE,KAAK,CAAC,EACjB,OAAO,OAAO,EACjB,OAAOD,EAAQ,OAAS,EAAIA,EAAU,MACxC,CAIA,SAASE,EAAcC,EAAe,CACpC,MAAO,CAAE,GAAIA,EAAM,MAAM,EAAG,EAAE,EAAG,OAAQA,EAAM,MAAM,EAAE,CAAE,CAC3D,CAEO,SAASC,EAAcZ,EAAwB,CACpD,IAAMC,EAAOD,EAAK,MAAM,GAAI,EACtBa,EAASH,EAAcT,EAAK,CAAC,CAAE,EAC/Ba,EAASJ,EAAcT,EAAK,CAAC,CAAE,EACrC,MAAO,CACL,OAAQY,EAAO,GACf,aAAcA,EAAO,OACrB,OAAQC,EAAO,GACf,aAAcA,EAAO,OACrB,cAAe,CACb,GAAID,EAAO,GACX,QAASZ,EAAK,CAAC,EACf,MAAO,CAACA,EAAK,CAAC,EACd,IAAK,CAACA,EAAK,CAAC,EACZ,KAAM,CAACA,EAAK,CAAC,EACb,KAAMA,EAAK,EAAE,GAAK,EACpB,EACA,cAAe,CACb,GAAIa,EAAO,GACX,QAASb,EAAK,CAAC,EACf,MAAO,CAACA,EAAK,EAAE,EACf,IAAK,CAACA,EAAK,EAAE,EACb,KAAM,CAACA,EAAK,EAAE,EACd,KAAMA,EAAK,EAAE,GAAK,EACpB,CACF,CACF,CAEO,SAASc,EAAQC,EAAgB,CACtC,MAAO,GAAGA,EAAK,MAAM,GAAGA,EAAK,YAAY,GAAGA,EAAK,MAAM,GAAGA,EAAK,YAAY,EAC7E,CASO,SAASC,EACdC,EACAC,EACAC,EACA,CACA,IAAMC,EAAQhB,GACZA,EAAQ,OAAS,GAAKA,EAAQ,UAAYe,EAAO,QAC7C,EACAf,EAAQ,KAAOe,EAAO,MACpB,GACAf,EAAQ,OAASe,EAAO,IACtB,EACA,EACJE,EAAW,IAAI,IAAIJ,CAAK,EACxBK,EAAQ,IAAI,IAClB,QAAWP,KAAQG,EACjB,GACED,EAAM,IAAIF,EAAK,MAAM,GACrBE,EAAM,IAAIF,EAAK,MAAM,GACrBK,EAAKL,EAAK,aAAa,EAAIK,EAAKL,EAAK,aAAa,IAAM,GACxD,CACAO,EAAM,IAAIR,EAAQC,CAAI,EAAGA,CAAI,EAC7B,QAAWX,IAAW,CAACW,EAAK,cAAeA,EAAK,aAAa,EACtDM,EAAS,IAAIjB,EAAQ,EAAE,GAC1BiB,EAAS,IAAIjB,EAAQ,GAAIA,CAAO,CAGtC,CAEF,QAAWW,KAAQG,EACbG,EAAS,IAAIN,EAAK,MAAM,GAAKM,EAAS,IAAIN,EAAK,MAAM,GACvDO,EAAM,IAAIR,EAAQC,CAAI,EAAGA,CAAI,EAGjC,MAAO,CAAE,SAAAM,EAAU,MAAAC,CAAM,CAC3B,CAqBO,SAASC,EACdC,EACAC,EACAN,EACA,CACA,IAAMO,EAAWtB,GACfA,EAAQ,UAAYe,EAAO,SAC3Bf,EAAQ,KAAOe,EAAO,OACtBf,EAAQ,OAASe,EAAO,IAC1B,MAAO,CACL,GAAGQ,EACDH,EAAK,OAAOpB,GAAWA,EAAQ,KAAO,CAAC,EACvCqB,EACAN,EAAO,IAAMA,EAAO,KACtB,EACA,GAAGQ,EACDH,EAAK,OAAOpB,GAAWA,EAAQ,OAAS,GAAKsB,EAAQtB,CAAO,CAAC,EAC7D,IAAI,IAAIoB,EAAK,IAAIpB,GAAWA,EAAQ,EAAE,CAAC,EACvC,CACF,CACF,CACF,CAEA,SAASuB,EACPN,EACAI,EACAG,EACA,CACA,IAAMC,EAAS,CAAC,GAAGR,CAAQ,EAAE,KAC3B,CAAC,EAAGS,IAAMC,EAAQ,EAAE,QAASD,EAAE,OAAO,GAAK,EAAE,MAAQA,EAAE,KACzD,EACME,EAA8C,CAAC,EACrD,QAAW5B,KAAWyB,EAAQ,CAC5B,IAAMI,EAAOD,EAAM,GAAG,EAAE,EAEtBC,GAAM,UAAY7B,EAAQ,SAC1BA,EAAQ,MAAQ6B,EAAK,KAAOL,GAE5BK,EAAK,SAAW7B,EAAQ,MAAQ6B,EAAK,KAAOR,EAAO,IAAIrB,EAAQ,EAAE,EACjE6B,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAK7B,EAAQ,GAAG,GAEzC4B,EAAM,KAAK,CACT,QAAS5B,EAAQ,QACjB,MAAOA,EAAQ,MACf,IAAKA,EAAQ,IACb,OAAQqB,EAAO,IAAIrB,EAAQ,EAAE,CAC/B,CAAC,CAEL,CACA,OAAO4B,EACJ,OAAOC,GAAQA,EAAK,MAAM,EAC1B,IAAI,CAAC,CAAE,QAAAC,EAAS,MAAAC,EAAO,IAAAC,CAAI,KAAmB,CAAE,QAAAF,EAAS,MAAAC,EAAO,IAAAC,CAAI,EAAE,CAC3E,CAIO,SAASC,EACdnB,EACAM,EACAQ,EACA,CACA,IAAMM,EAAUlC,GACdoB,EAAK,IAAIpB,EAAQ,EAAE,GACnB4B,EAAM,KACJC,GACEA,EAAK,UAAY7B,EAAQ,SACzBA,EAAQ,OAAS6B,EAAK,OACtB7B,EAAQ,KAAO6B,EAAK,GACxB,EACF,OAAOf,EAAM,OACXH,GAAQuB,EAAOvB,EAAK,aAAa,GAAKuB,EAAOvB,EAAK,aAAa,CACjE,CACF,CAUA,IAAMwB,GAAU,kCAEhB,SAASC,GAAcpC,EAAsB,CAC3C,GAAM,CAAE,GAAAqC,EAAI,QAAAP,EAAS,MAAAC,EAAO,IAAAC,EAAK,KAAAM,EAAM,KAAAC,CAAK,EAAIvC,EAC1CwC,EAAQD,EAAK,MAAM,GAAG,EAAE,OAAOrC,GAAKiC,GAAQ,KAAKjC,CAAC,CAAC,EACnDuC,EAAQD,EAAM,SAAW,EAAI,GAAK,IAAKA,EAAM,KAAK,GAAI,CAAC,GAC7D,MAAO,KAAMH,CAAE,WAAaL,EAAMD,CAAK,SAAUD,CAAO,SAAUC,CAAK,SAAUO,CAAI,GAAGG,CAAK,EAC/F,CAEA,SAASC,GAAW/B,EAAgB,CAClC,GAAM,CAAE,OAAAH,EAAQ,aAAAmC,EAAc,OAAAlC,EAAQ,aAAAmC,CAAa,EAAIjC,EACvD,MAAO,KAAMH,CAAM,IAAKmC,CAAY,IAAKlC,CAAM,IAAKmC,CAAY,KAClE,CAIA,SAASjB,EAAQkB,EAAWnB,EAAW,CACrC,OAAOmB,EAAInB,EAAI,GAAKmB,EAAInB,EAAI,EAAI,CAClC,CAIO,SAASoB,EACd7B,EACAC,EACA,CACA,IAAM6B,EAAiB,CAAC,GAAG9B,EAAS,OAAO,CAAC,EAAE,KAC5C,CAAC4B,EAAGnB,IACFC,EAAQkB,EAAE,QAASnB,EAAE,OAAO,GAAKmB,EAAE,MAAQnB,EAAE,OAASC,EAAQkB,EAAE,GAAInB,EAAE,EAAE,CAC5E,EACMsB,EAAc,CAAC,GAAG9B,EAAM,KAAK,CAAC,EAAE,KAAK,CAAC2B,EAAGnB,IAAMC,EAAQkB,EAAGnB,CAAC,CAAC,EAClE,MAAO,CACL,aACA,GAAGqB,EAAe,IAAI3C,GAAKgC,GAAchC,CAAC,CAAC,EAC3C,GAAG4C,EAAY,IAAIC,GAAKP,GAAWxB,EAAM,IAAI+B,CAAC,CAAE,CAAC,CACnD,EAAE,KAAK;AAAA,CAAI,CACb,CC7SA,IAAAC,EAAgC,SA0CzB,SAASC,GAAYC,EAAc,CACxC,IAAIC,EAAK,GACT,QAASC,EAAI,EAAGA,EAAI,EAAGA,IACrBD,EAAKD,EAAK,QAAQ,IAAMC,EAAK,CAAC,EAEhC,OAAOD,EAAK,MAAMC,EAAK,EAAGD,EAAK,QAAQ,IAAMC,EAAK,CAAC,CAAC,CACtD,CAEO,SAASE,GAAaH,EAAuB,CAClD,IAAMI,EAAIJ,EAAK,MAAM,IAAM,CAAC,EAC5B,MAAO,CACL,WAAY,CAACI,EAAE,CAAC,EAChB,KAAMA,EAAE,CAAC,EACT,UAAW,CAACA,EAAE,CAAC,EACf,UAAW,CAACA,EAAE,CAAC,EACf,MAAO,CAACA,EAAE,CAAC,EACX,EAAG,CAACA,EAAE,CAAC,EACP,IAAKA,EAAE,CAAC,CACV,CACF,CASA,SAASC,EAAWL,EAAcM,EAAa,CAC7C,IAAMC,EAAQ,IAAI,OAAO,YAAYD,CAAG,WAAW,EAAE,KAAKN,CAAI,EAC9D,OAAOO,EAAQ,CAACA,EAAM,CAAC,EAAK,MAC9B,CASO,SAASC,GAAWC,EAA6B,CACtD,IAAMC,EAAqB,CAAE,WAAY,CAAC,EAAG,WAAY,CAAC,CAAE,EAC5D,QAAWV,KAAQS,EAAO,CACxB,GAAM,CAACE,EAAKC,EAAQ,EAAE,EAAIZ,EAAK,MAAM,GAAI,EACrCW,IAAQ,aACVD,EAAO,WAAW,KAAKE,CAAK,EACnBD,IAAQ,aACjBD,EAAO,WAAW,KAAKE,CAAK,GAE5BF,EAAO,QAAUL,EAAWL,EAAM,OAAO,EACzCU,EAAO,UAAYL,EAAWL,EAAM,SAAS,EAEjD,CACA,OAAOU,CACT,CAUO,SAASG,GAAeC,EAA6BC,EAAe,CACzE,OAAOD,IAAY,OAAY,EAAI,KAAK,IAAI,EAAG,KAAK,KAAKA,EAAUC,CAAK,CAAC,CAC3E,CAIO,SAASC,EAAgBC,EAAeF,EAAeG,EAAW,EAAG,CAC1E,OAAO,KAAK,IAAI,GAAI,KAAK,MAAMD,EAAQF,CAAK,EAAIG,GAAYH,CAAK,CACnE,CAIO,SAASI,GACdC,EACAC,EACA,CACA,OAAOD,IAAW,QAAaA,EAAO,SAAW,EAC7C,OACCE,GACCC,EAAmBD,EAAMD,CAAkB,GAC3CD,EAAO,KAAKI,GAAUD,EAAmBD,EAAME,CAAM,CAAC,CAC9D,CAEO,SAASC,GACdC,EACAC,EACAC,EAAM,IAAI,WAAWD,CAAC,EACtBE,EAAM,IAAI,WAAWF,CAAC,EACtB1B,EAAK,EACL,CACA,IAAI6B,EAAO,EACP,EAAI7B,EACJ8B,EAAI,EACJC,EAAM,GACV,QAASC,EAAI,EAAGA,GAAKP,EAAI,OAAQO,IAAK,CACpC,IAAMC,EAAKD,EAAIP,EAAI,OAASA,EAAI,WAAWO,CAAC,EAAI,GAChD,GAAIC,IAAO,GAAI,CACb,IAAMC,EAAIH,EAAM,CAACD,EAAIA,EACfK,EAAID,EAAI,EACdN,EAAI,CAAC,EAAIO,EACTN,IAASK,EAAIC,GAAK,EAClBR,EAAI,GAAG,EAAIE,EACXC,EAAI,EACJC,EAAM,EACR,MAAWE,IAAO,GAChBF,EAAM,GAEND,EAAIA,EAAI,IAAMG,EAAK,GAEvB,CACA,MAAO,CAAE,IAAAN,EAAK,IAAAC,CAAI,CACpB,CAUO,SAASQ,GAAWC,EAAiB,CAC1C,IAAMC,EAAS,IAAI,IACnB,QAAWC,KAAOF,EAAM,CACtB,IAAM3B,EAAM,GAAG6B,EAAI,IAAI,IAAKA,EAAI,SAAS,GACnCC,EAAOF,EAAO,IAAI5B,CAAG,EACvB8B,EACFA,EAAK,KAAKD,CAAG,EAEbD,EAAO,IAAI5B,EAAK,CAAC6B,CAAG,CAAC,CAEzB,CACA,IAAME,EAAkB,CAAC,EACzB,QAAWC,KAAUJ,EAAO,OAAO,EAAG,CACpCI,EAAO,KAAK,CAAC,EAAGC,IAAM,EAAE,MAAQA,EAAE,KAAK,EACvC,IAAIC,EAAO,EACX,QAASC,EAAI,EAAGA,GAAKH,EAAO,OAAQG,KAEhCA,IAAMH,EAAO,QACbA,EAAOG,CAAC,EAAG,QAAUH,EAAOG,EAAI,CAAC,EAAG,MAAQ,KAE5CJ,EAAK,KAAKK,GAAUJ,EAAO,MAAME,EAAMC,CAAC,CAAC,CAAC,EAC1CD,EAAOC,EAGb,CACA,OAAOJ,CACT,CAEA,SAASK,GAAUJ,EAA4B,CAC7C,IAAMhB,EAAIgB,EAAO,OAAO,CAACK,EAAKf,IAAMe,EAAMf,EAAE,EAAG,CAAC,EAC1CL,EAAM,IAAI,WAAWD,CAAC,EACtBE,EAAM,IAAI,WAAWF,CAAC,EACxB1B,EAAK,EACT,QAAWgC,KAAKU,EACdlB,GAAYQ,EAAE,IAAKA,EAAE,EAAGL,EAAKC,EAAK5B,CAAE,EACpCA,GAAMgC,EAAE,EAEV,MAAO,CAAE,KAAMU,EAAO,CAAC,EAAG,KAAM,UAAWA,EAAO,CAAC,EAAG,UAAW,IAAAf,EAAK,IAAAC,CAAI,CAC5E,CAkBO,SAASoB,GAAQP,EAAiBQ,EAA8B,CACrE,IAAMC,EAAYC,GAA+BA,GAAM,WAAa,GAC9DC,EAAO,IAAI,IACjB,OAAW,CAACC,EAAIF,CAAI,IAAKF,EACnBE,EAAK,UACPC,EAAK,IAAIC,CAAE,EAGf,IAAMC,EAAyD,CAAC,EAChE,QAAWC,KAAOd,EAAM,CACtB,GAAM,CAAE,IAAAd,CAAI,EAAI4B,EACZC,EAAQ,GACRC,EAAO,GACX,QAASZ,EAAI,EAAGA,EAAIlB,EAAI,OAAQkB,IAC1BK,EAASD,EAAM,IAAItB,EAAIkB,CAAC,CAAE,CAAC,IACzBW,EAAQ,IACVA,EAAQX,GAEVY,EAAOZ,GAGX,GAAIW,GAAS,EAAG,CACd,QAASX,EAAIW,EAAOX,GAAKY,EAAMZ,IAC7BO,EAAK,IAAIzB,EAAIkB,CAAC,CAAE,EAElBS,EAAM,KAAK,CAAE,IAAAC,EAAK,MAAAC,EAAO,KAAAC,CAAK,CAAC,CACjC,CACF,CACA,IAAMC,EAAUL,GAAe,CAC7B,IAAMF,EAAOF,EAAM,IAAII,CAAE,EACzB,OAAOF,IAAS,OAAY,EAAIA,EAAK,IAAMA,EAAK,KAClD,EACMQ,EAA4B,CAAC,EACnC,OAAW,CAAE,IAAAJ,EAAK,MAAO,EAAG,KAAM,CAAE,IAAKD,EAAO,CAC9C,GAAM,CAAE,IAAA3B,EAAK,IAAAC,CAAI,EAAI2B,EACjBC,EAAQ,EACRC,EAAO,EACX,KAAOD,EAAQ,GAAKJ,EAAK,IAAIzB,EAAI6B,EAAQ,CAAC,CAAE,GAC1CA,IAEF,KAAOC,EAAO9B,EAAI,OAAS,GAAKyB,EAAK,IAAIzB,EAAI8B,EAAO,CAAC,CAAE,GACrDA,IAEF,IAAIG,EAAWL,EAAI,UACnB,QAASV,EAAI,EAAGA,EAAIW,EAAOX,IACzBe,GAAYF,EAAO/B,EAAIkB,CAAC,CAAE,EAE5B,IAAIgB,EAASD,EACb,QAASf,EAAIW,EAAOX,GAAKY,EAAMZ,IAC7BgB,GAAUH,EAAO/B,EAAIkB,CAAC,CAAE,EAE1Bc,EAAU,KAAK,CACb,KAAMJ,EAAI,KACV,SAAAK,EACA,OAAAC,EACA,IAAKlC,EAAI,SAAS6B,EAAOC,EAAO,CAAC,EACjC,IAAK7B,EAAI,SAAS4B,EAAOC,EAAO,CAAC,CACnC,CAAC,CACH,CACA,MAAO,CAAE,KAAAL,EAAM,UAAAO,CAAU,CAC3B,CAEO,SAASG,GAAW,CAAE,KAAAzC,EAAM,SAAAuC,EAAU,OAAAC,EAAQ,IAAAlC,EAAK,IAAAC,CAAI,EAAiB,CAC7E,GAAM,CAACmC,EAAQC,EAAW,GAAGC,CAAM,EAAI5C,EAAK,MAAM,GAAG,EAC/C6C,EAAQ,IAAI,MAAcvC,EAAI,MAAM,EAC1C,QAASkB,EAAI,EAAGA,EAAIlB,EAAI,OAAQkB,IAC9BqB,EAAMrB,CAAC,GAAKjB,EAAIiB,CAAC,EAAI,IAAM,KAAOlB,EAAIkB,CAAC,EAEzC,MAAO,KAAMkB,CAAM,IAAKC,CAAS,IAAKC,EAAO,KAAK,GAAG,CAAC,IAAKL,CAAQ,IAAKC,CAAM,IAAKK,EAAM,KAAK,EAAE,CAAC,EACnG,CAGA,SAASC,EAAKpE,EAAc2B,EAAW0C,EAAe,CACpD,IAAIpE,EAAK,GACT,QAASC,EAAI,EAAGA,EAAIyB,EAAGzB,IACrBD,EAAKA,IAAO,IAAMC,EAAI,EAAI,GAAKF,EAAK,QAAQ,IAAMC,EAAK,CAAC,EACxDoE,EAAInE,CAAC,EAAID,EAEX,OAAOoE,CACT,CAQO,IAAMC,EAAN,KAAgB,CAKrB,YAAoBC,EAAoB,CAApB,YAAAA,EAJpB,KAAS,MAAQ,IAAI,IACrB,KAAQ,MAAkB,CAAC,EAC3B,KAAiB,EAAc,CAAC,CAES,CAEzC,QAAQvE,EAAc,CACpB,IAAMwE,EAAIJ,EAAKpE,EAAM,EAAG,KAAK,CAAC,EACxBsD,EAAK,CAACtD,EAAK,MAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,CAAC,EACtC,GAAI,CAAC,KAAK,MAAM,IAAIlB,CAAE,EAAG,CACvB,IAAMmB,EAAO,CAACzE,EAAK,MAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,CAAC,EAClCE,EAAU1E,EAAK,MAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,CAAC,EACpCvD,EAAQ,CAACjB,EAAK,MAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,CAAC,EACnCG,EAAM,CAAC3E,EAAK,MAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,IAAM,GAAK,OAAYA,EAAE,CAAC,CAAC,EAC3D,CAAE,OAAAD,CAAO,EAAI,KACnB,KAAK,MAAM,IAAIjB,EAAI,CACjB,KAAAmB,EACA,QAAAC,EACA,MAAAzD,EACA,IAAA0D,EACA,SACEF,IAAS,GACTC,IAAYH,EAAO,SACnBI,EAAMJ,EAAO,MAAQA,EAAO,SAC5BtD,EAAQsD,EAAO,IAAMA,EAAO,OAChC,CAAC,CACH,CACF,CAGA,QAAQvE,EAAc,CACpB,IAAMwE,EAAIJ,EAAKpE,EAAM,EAAG,KAAK,CAAC,EAC9B,KAAK,MAAM,KACT4E,EAAS5E,EAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,CAAE,EAC/BI,EAAS5E,EAAMwE,EAAE,CAAC,EAAK,EAAGA,EAAE,CAAC,IAAM,GAAKxE,EAAK,OAASwE,EAAE,CAAC,CAAE,CAC7D,CACF,CAOA,OAAOnB,EAAmBO,EAA2B,CACnD,IAAMiB,EAAsC,CAAC,EAC7C,QAAWvB,KAAMD,EAAM,CACrB,IAAMD,EAAO,KAAK,MAAM,IAAIE,CAAE,EAC1BF,GACFyB,EAAK,KAAK,CAAE,GAAGzB,EAAM,GAAAE,CAAG,CAAC,CAE7B,CACAuB,EAAK,KAAK,CAACC,EAAGC,IACZD,EAAE,QAAUC,EAAE,QACV,GACAD,EAAE,QAAUC,EAAE,QACZ,EACAD,EAAE,MAAQC,EAAE,OAASD,EAAE,GAAKC,EAAE,EACtC,EACA,IAAMtE,EAAQ,CAAC,YAAa,EAC5B,OAAW,CAAE,GAAA6C,EAAI,QAAAoB,EAAS,MAAAzD,EAAO,IAAA0D,EAAK,KAAAF,CAAK,IAAKI,EAC9CpE,EAAM,KACJ,KAAM6C,CAAE,WAAaqB,EAAM1D,CAAK,SAAUyD,CAAO,SAAUzD,CAAK,SAAUwD,CAAI,EAChF,EAEF,IAAMO,EAAO,IAAI,IACXC,EAAkB,CAAC,EACzB,QAASnC,EAAI,EAAGA,EAAI,KAAK,MAAM,OAAQA,GAAK,EAAG,CAC7C,IAAMoC,EAAI,KAAK,MAAMpC,CAAC,EAChBF,EAAI,KAAK,MAAME,EAAI,CAAC,EACpBqC,EAAS,KAAK,MAAMD,EAAI,CAAC,EACzBE,EAAS,KAAK,MAAMxC,EAAI,CAAC,EAC/B,GAAIS,EAAK,IAAI8B,CAAM,GAAK9B,EAAK,IAAI+B,CAAM,EAAG,CACxC,IAAMpF,EAAO,KAAMmF,CAAM,IAAKD,EAAI,EAAI,IAAM,GAAG,IAAKE,CAAM,IAAKxC,EAAI,EAAI,IAAM,GAAG,MAC3EoC,EAAK,IAAIhF,CAAI,IAChBgF,EAAK,IAAIhF,CAAI,EACbiF,EAAM,KAAKjF,CAAI,EAEnB,CACF,CACA,OAAAiF,EAAM,KAAK,EACJ,CACL,GAAGxE,EACH,GAAGwE,EACH,GAAG,KAAK,eAAerB,CAAS,EAAE,IAAIG,EAAU,CAClD,EAAE,KAAK;AAAA,CAAI,CACb,CAKQ,eAAeH,EAA2B,CAChD,GAAM,CAAE,QAAAc,CAAQ,EAAI,KAAK,OACzB,MAAO,CAAC,GAAGd,CAAS,EAAE,KACpB,CAACsB,EAAGtC,IACF,EAAOA,EAAE,OAAS8B,GAAW,EAAOQ,EAAE,OAASR,KAC9CQ,EAAE,KAAOtC,EAAE,KAAO,GAAKsC,EAAE,KAAOtC,EAAE,KAAO,EAAIsC,EAAE,SAAWtC,EAAE,SACjE,CACF,CACF,EAEA,SAASgC,EAAS5E,EAAc6C,EAAcwC,EAAY,CACxD,MACE,CAACrF,EAAK,MAAM6C,EAAMwC,EAAK,CAAC,EAAI,GAAKrF,EAAK,WAAWqF,EAAK,CAAC,IAAM,GAAK,EAAI,EAE1E,CAWO,SAASC,GACdhD,EACAiD,EACAhB,EACAxD,EACAyE,EACA,CACA,IAAIC,EAAQ,EACNC,EAAW,IAAI,IACfC,EAAQ,IAAI,IAClB,QAAWnD,KAAOF,EAChBmD,GAASjD,EAAI,EACbkD,EAAS,IAAIlD,EAAI,YAAakD,EAAS,IAAIlD,EAAI,UAAU,GAAK,GAAKA,EAAI,CAAC,EACxEmD,EAAM,IAAInD,EAAI,IAAI,EAEpB,GAAIiD,GAASF,EACX,OAEF,IAAMK,EAAWrB,EAAO,IAAMA,EAAO,MACjCsB,EAAO,EACPC,EAAS,EACb,QAAWC,IAAM,CAAC,GAAGL,EAAS,KAAK,CAAC,EAAE,KAAK,CAACR,EAAGtC,IAAMsC,EAAItC,CAAC,EAAG,CAE3D,GADAiD,GAAQH,EAAS,IAAIK,CAAE,EACnBF,EAAON,EACT,MAEFO,EAAS,KAAK,IAAIA,EAAQC,EAAKhF,EAAQwD,EAAO,KAAK,CACrD,CACA,IAAMyB,EACJ,CAACR,GAAYG,EAAM,KAAO,GAAM,EAAIF,EAASE,EAAM,MAAQJ,EACvDU,EAAQ,IAAIC,EAAeX,EAAQK,EAAU,KAAK,IAAIE,EAAQ,CAAC,CAAC,EACtE,OAAAG,EAAM,QACJH,EAAS,EACL,uBAAoB,mBAAgBA,CAAM,CAAC,GAAGE,EAAW,gCAAkC,EAAE,oBAC7F,yCAAyCR,EAAW,mBAAqB,iBAAiB,KAAKK,EAAK,eAAe,CAAC,2BAA2BN,EAAO,eAAe,CAAC,6BACrKU,CACT,CAUA,eAAsBE,GACpBC,EACAb,EACAhB,EACAxD,EACA,CACA,IAAMsF,EAAQ,MAAMD,EAAQ7B,EAAO,GAAG,EACtC,GAAI8B,GAASd,EACX,OAEF,IAAIO,EAAS,EACTQ,EACJ,QACMP,EAAK,KAAK,MAAMxB,EAAO,MAAQxD,CAAK,EAAIA,EAC5CgF,EAAKxB,EAAO,IACZwB,GAAMhF,EACN,CACA,IAAM8E,EAAO,MAAMO,EAAQL,EAAK,CAAC,EAEjC,GADAO,IAAUT,EACNA,EAAON,EACT,MAEFO,EAASC,EAAKhF,EAAQwD,EAAO,KAC/B,CACA,IAAMqB,EAAWrB,EAAO,IAAMA,EAAO,MAC/B0B,EAAQ,IAAIC,EAAeX,EAAQK,EAAU,KAAK,IAAIE,EAAQ,CAAC,CAAC,EACtE,OAAAG,EAAM,QACJH,EAAS,EACL,uBAAoB,mBAAgBA,CAAM,CAAC,oBAC3C,iCAAiCS,EAAUD,GAASD,CAAK,CAAC,2BAA2BE,EAAUhB,CAAM,CAAC,IACrGU,CACT,CAEA,IAAMM,EAAaF,GAAkB,IAAIA,EAAQ,KAAK,QAAQ,CAAC,CAAC,MF/ahE,SAASG,GAAaC,EAAyB,CAC7C,OAAOA,EAAS,OAAOC,GAAWA,EAAQ,KAAO,CAAC,CACpD,CAKA,SAASC,GAAWC,EAAiBC,EAAeC,EAAa,CAC/D,GAAI,CAAC,OAAO,SAASD,CAAK,GAAK,CAAC,OAAO,SAASC,CAAG,EACjD,MAAM,IAAI,MACR,GAAGF,CAAO,IAAIC,CAAK,IAAIC,CAAG,uDAC5B,CAEJ,CAEA,eAAeC,EACbC,EACAJ,EACAC,EACAC,EACAG,EACA,CACA,OAAAN,GAAWC,EAASC,EAAOC,CAAG,EACvBE,EAAK,SAASJ,EAASC,EAAOC,EAAKG,CAAI,CAChD,CAUA,IAAMC,GAAe,IAEAC,EAArB,cAA8C,wBAA+C,CAMpF,YACLC,EACAC,EACAC,EACA,CACA,MAAMF,EAAQC,EAAeC,CAAa,EAkC5C,KAAQ,cAAa,eAAY,CAC/B,MAAO,MAAML,GAAQ,CACnB,IAAMM,EAAQ,KAAK,KAAK,MAClBC,EAASC,GAAWF,EAAQ,MAAMA,EAAM,eAAeN,CAAI,EAAI,CAAC,CAAC,EACjES,EAAe,KAAK,QAAQ,WAAW,EACvCC,EAAQH,EAAO,OAASE,EAC9B,MAAO,CACL,GAAGF,EACH,MAAAG,EACA,SAAUC,GAAeJ,EAAO,QAASG,CAAK,CAChD,CACF,CACF,CAAC,EA7CC,KAAK,KAAO,KAAK,UAAU,CAAC,CAAC,CAC/B,CAZA,YAAc,aAAe,CAAC,cAAe,aAAa,EAiBlD,UAAUE,EAA6B,CAC7C,IAAMpB,EAAWqB,EACf,KACA,CAAC,GAAGD,EAAO,kBAAkB,EAC7B,CAAC,GAAGA,EAAO,eAAe,CAC5B,EACME,EAA8B,KAAK,QAAQ,eAAe,EAC1DC,EACJH,EAAM,SAAW,IAChB,EAAE,QAASE,IAAkBA,EAAc,MAAQ,IACtD,MAAO,CACL,SAAAtB,EACA,MAAOqB,EACL,KACA,CAAC,GAAGD,EAAO,eAAe,EAC1B,CAAC,GAAGA,EAAO,YAAY,CACzB,EACA,MAAOG,EACHF,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,OACJ,SAAU,IAAIG,EAAcxB,EAAU,IAAI,CAC5C,CACF,CAmBA,MAAc,eAAeI,EAAeI,EAAmB,CAC7D,GAAM,CAAE,MAAAU,EAAO,SAAAO,CAAS,EAAI,MAAM,KAAK,WAAWjB,CAAI,EACtD,OAAOkB,EAAgBtB,EAAOc,EAAOO,CAAQ,CAC/C,CAMA,MAAM,kBAAkBjB,EAAoB,CAAC,EAAG,CAC9C,GAAI,CAAC,KAAK,KAAK,MACb,OAEF,GAAM,CAAE,WAAAmB,CAAW,EAAI,MAAM,KAAK,WAAWnB,CAAI,EACjD,OAAOmB,EAAW,OAAS,EAAIA,EAAa,MAC9C,CAEQ,MAAMC,EAAqB,OAAQ,CACzC,OAAIA,IAAS,OACJ,KAAK,MAEd,KAAK,SAAW,KAAK,UAAU,CAAC,QAAQ,CAAC,EAClC,KAAK,OACd,CAEA,MAAM,YAAYpB,EAAoB,CAAC,EAAG,CACxC,OAAO,KAAK,KAAK,SAAS,iBAAiBA,CAAI,CACjD,CAEA,MAAa,mBAAoB,CAC/B,MAAO,EACT,CAEA,YAAYqB,EAAerB,EAAoB,CAAC,EAAG,CACjD,GAAM,CAAE,OAAAsB,EAAQ,eAAAC,CAAe,EAAIvB,EACnC,SAAO,qBAA0B,MAAMwB,GAAY,CACjD,IAAMC,EAAe,MAAM,KAAK,KAAK,SAAS,QAAQJ,EAAOrB,CAAI,EACjE,GAAIyB,IAAiB,OAAW,CAG9B,IAAM7B,EAAQ,KAAK,KAAK,MACpB,MAAM,KAAK,eAAeyB,EAAM,MAAOrB,CAAI,EAC3CqB,EAAM,MACV,QAAM,gBAAa,uBAAwBE,EAAgB,IACzDzB,EAAS,KAAK,KAAK,SAAU2B,EAAc7B,EAAOyB,EAAM,IAAK,CAC3D,OAAAC,EACA,aAAcI,GAAQ,CACpB,GAAM,CAAE,QAAAjC,EAAS,SAAAkC,CAAS,EAAIC,EAAgBF,CAAI,EAIlD,GAAIC,GAAYlC,EAAQ,UAAYgC,EAClC,OAMF,IAAMI,EAAUC,EAAerC,CAAO,EACtC+B,EAAS,KACP,IAAI,gBAAc,CAChB,SAAU/B,EAAQ,GAClB,QAAS4B,EAAM,QACf,MAAO5B,EAAQ,MACf,IAAKA,EAAQ,IACb,KAAMA,EAAQ,GACd,KAAM,UACN,KAAMA,EAAQ,KACd,WAAYA,EAAQ,QACpB,GAAIoC,GAAW,CAAE,QAAAA,EAAS,YAAaA,EAAQ,MAAO,CACxD,CAAC,CACH,CACF,CACF,CAAC,CACH,CACF,CACAL,EAAS,SAAS,CACpB,EAAGF,CAAM,CACX,CAgBA,MAAM,YAAYS,EAAgB/B,EAA+B,CAAC,EAAG,CACnE,GAAM,CAAE,KAAAgC,EAAO,EAAG,OAAAV,EAAQ,KAAAF,CAAK,EAAIpB,EAC7BiC,EAAQ,KAAK,MAAMb,CAAI,EACvB5B,EAAW,IAAI,IACf0C,EAAQ,IAAI,IACZT,EAAe,MAAMQ,EAAM,SAAS,QAAQF,EAAQ,CAAE,OAAAT,CAAO,CAAC,EAE9Da,EAAe,MACnBxC,EACAC,EACAC,IACG,CACH,IAAMuC,EAAyB,CAAC,EAChC,aAAMtC,EAASmC,EAAM,MAAOtC,EAASC,EAAOC,EAAK,CAC/C,OAAAyB,EACA,aAAcI,GAAQ,CACpB,IAAMW,EAAOC,EAAcZ,CAAI,EAC/BQ,EAAM,IAAIK,EAAQF,CAAI,EAAGA,CAAI,EAC7B,QAAW5C,IAAW,CAAC4C,EAAK,cAAeA,EAAK,aAAa,EACtD7C,EAAS,IAAIC,EAAQ,EAAE,IAC1BD,EAAS,IAAIC,EAAQ,GAAIA,CAAO,EAChC2C,EAAQ,KAAK3C,CAAO,EAG1B,CACF,CAAC,EACM2C,CACT,EAEA,GAAIX,IAAiB,OACnB,MAAM,IAAI,MACR,GAAGM,EAAO,YAAY,IAAIA,EAAO,OAAO,iFAAiFA,EAAO,YAAY,8CAC9I,EAEF,GAAIE,EAAM,MACR,OAAO,KAAK,aAAaA,EAAOA,EAAM,MAAOR,EAAcM,EAAQ/B,CAAI,EAEzE,IAAMwC,EAAS,CAAE,SAAU,EAAM,EAYjC,GAXA,MAAM1C,EAASmC,EAAM,SAAUR,EAAcM,EAAO,MAAOA,EAAO,IAAK,CACrE,OAAAT,EACA,aAAcI,GAAQ,CACpB,IAAMe,EAAMb,EAAgBF,CAAI,EAChCc,EAAO,WAAaC,EAAI,SACxBjD,EAAS,IAAIiD,EAAI,QAAQ,GAAIA,EAAI,OAAO,CAC1C,CACF,CAAC,EAIGD,EAAO,SAAU,CACnB,IAAME,EAAoB,CAAC,EAC3B,MAAM5C,EAASmC,EAAM,MAAOR,EAAcM,EAAO,MAAOA,EAAO,IAAK,CAClE,OAAAT,EACA,aAAcI,GAAQ,CACpBgB,EAAM,KAAKJ,EAAcZ,CAAI,CAAC,CAChC,CACF,CAAC,EACD,IAAMiB,EAAMC,EAAYpD,EAAUkD,EAAO,CACvC,QAASjB,EACT,MAAOM,EAAO,MACd,IAAKA,EAAO,GACd,CAAC,EACD,OAAOc,EAAeF,EAAI,SAAUA,EAAI,KAAK,CAC/C,CACA,IAAIG,EAAWvD,GACb,MAAM4C,EAAaV,EAAcM,EAAO,MAAOA,EAAO,GAAG,CAC3D,EACA,QAASgB,EAAM,EAAGA,EAAMf,EAAMe,IAAO,CAMnC,IAAMX,EAAU,MAAM,QAAQ,IAC5BU,EAAS,IAAIrD,GACX0C,EAAa1C,EAAQ,QAASA,EAAQ,MAAOA,EAAQ,GAAG,CAC1D,CACF,EACAqD,EAAWvD,GAAa6C,EAAQ,KAAK,CAAC,CACxC,CACA,GAAIJ,EAAO,EAAG,CACZ,IAAMgB,EAAQC,EACZ,CAAC,GAAGzD,EAAS,OAAO,CAAC,EACrB,IAAI,IAAIsD,EAAS,IAAIrD,GAAWA,EAAQ,EAAE,CAAC,EAC3C,CAAE,QAASgC,EAAc,MAAOM,EAAO,MAAO,IAAKA,EAAO,GAAI,CAChE,EACMW,EAAoB,CAAC,EAC3B,MAAM,QAAQ,IACZM,EAAM,IAAIE,GACRpD,EAASmC,EAAM,MAAOiB,EAAK,QAASA,EAAK,MAAOA,EAAK,IAAK,CACxD,OAAA5B,EACA,aAAcI,GAAQ,CACpBgB,EAAM,KAAKJ,EAAcZ,CAAI,CAAC,CAChC,CACF,CAAC,CACH,CACF,EACA,QAAWW,KAAQc,EAAaT,EAAOlD,EAAUwD,CAAK,EAAG,CACvDd,EAAM,IAAIK,EAAQF,CAAI,EAAGA,CAAI,EAC7B,QAAW5C,IAAW,CAAC4C,EAAK,cAAeA,EAAK,aAAa,EACtD7C,EAAS,IAAIC,EAAQ,EAAE,GAC1BD,EAAS,IAAIC,EAAQ,GAAIA,CAAO,CAGtC,CACF,CAEA,OAAOoD,EAAerD,EAAU0C,CAAK,CACvC,CAQA,MAAc,aACZD,EACA3B,EACAX,EACAoC,EACA/B,EACA,CACA,GAAM,CAAE,OAAAsB,EAAQ,WAAAH,CAAW,EAAInB,EACzB,CAAE,MAAAU,EAAO,SAAAO,CAAS,EAAI,MAAM,KAAK,WAAW,CAAE,OAAAK,CAAO,CAAC,EACtD8B,EAAiB,KAAK,QAAQ,gBAAgB,EAC9CC,EAAOC,GACXnC,GAAY,IAAIoC,GAAQC,EAAmB,KAAMD,CAAI,CAAC,EACtDE,EAAe9D,CAAO,CACxB,EACM+D,EAAOxC,EAAgBa,EAAO,MAAOrB,EAAOO,CAAQ,EACpD0C,EAAQ,CAACrD,EAAO2B,EAAM,SAAUA,EAAM,KAAK,EAC3C2B,EAAW,MAAMC,GACrB,MAAMhE,IACJH,GAAWC,EAAS+D,EAAM7D,CAAG,GACf,MAAM,QAAQ,IAC1B8D,EAAM,IAAI5D,GACRA,EAAK,gBAAgB,CAAC,CAAE,QAAAJ,EAAS,MAAO+D,EAAM,IAAA7D,CAAI,CAAC,EAAG,CAAE,OAAAyB,CAAO,CAAC,CAClE,CACF,GACa,OAAO,CAACwC,EAAKC,KAAUD,EAAMC,GAAO,CAAC,GAEpD,KAAK,QAAQ,gBAAgB,EAC7BhC,EACArB,CACF,EACA,GAAIkD,EACF,MAAMA,EAER,IAAMI,EAAQ,IAAI,gBACZC,EAAO,IAAM,CACjBD,EAAM,MAAM1C,GAAQ,MAAM,CAC5B,EACAA,GAAQ,iBAAiB,QAAS2C,EAAM,CAAE,KAAM,EAAK,CAAC,EACtD,IAAMC,EAAkB,CAAC,EACnBC,EAAQ,IAAIC,EAAU,CAC1B,QAAAzE,EACA,MAAOoC,EAAO,MACd,IAAKA,EAAO,IACZ,QAAS9B,EACX,CAAC,EACKoE,EAAO,CACXtE,EACAuE,IAEAxE,EAASC,EAAMJ,EAAS+D,EAAM3B,EAAO,IAAK,CACxC,OAAQiC,EAAM,OACd,aAAAM,CACF,CAAC,EACH,GAAI,CACF,MAAM,QAAQ,IAAI,CAChBD,EAAK/D,EAAOoB,GAAQ,EACd2B,IAAS,QAAaA,EAAKkB,GAAY7C,CAAI,CAAC,IAC9CwC,EAAK,KAAKM,GAAa9C,CAAI,CAAC,CAEhC,CAAC,EAAE,KAAK,IAAM,CACZ,IAAM+C,EAAQC,GACZR,EACAd,EACArB,EACArB,EACA2C,IAAS,MACX,EACA,GAAIoB,EACF,MAAMA,CAEV,CAAC,EACDJ,EAAKpC,EAAM,SAAUP,GAAQ,CAC3ByC,EAAM,QAAQzC,CAAI,CACpB,CAAC,EACD2C,EAAKpC,EAAM,MAAOP,GAAQ,CACxByC,EAAM,QAAQzC,CAAI,CACpB,CAAC,CACH,CAAC,CACH,OAAS+C,EAAO,CACd,MAAAT,EAAM,MAAM,EACNS,CACR,QAAE,CACAnD,GAAQ,oBAAoB,QAAS2C,CAAI,CAC3C,CACA,GAAM,CAAE,KAAAU,GAAM,UAAAC,EAAU,EAAIC,GAAQC,GAAWZ,CAAI,EAAGC,EAAM,KAAK,EACjE,OAAOA,EAAM,OAAOQ,GAAMC,EAAS,CACrC,CACF",
+  "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", "b", "compare", "spans", "span", "refName", "start", "end", "closingLinks", "inside", "GFA_TAG", "formatSegment", "id", "rank", "tags", "valid", "extra", "formatLink", "sourceStrand", "targetStrand", "a", "formatSubgraph", "sortedSegments", "sortedLinks", "k", "import_util", "walkRowName", "line", "at", "k", "parseWalkRow", "c", "integerTag", "tag", "match", "walkHeader", "lines", "header", "key", "value", "lookbackChunks", "maxNode", "chunk", "chunkQueryStart", "start", "lookback", "walkNameFilter", "wanted", "referenceHaplotype", "name", "panSNMatchesPrefix", "prefix", "decodeSteps", "enc", "n", "ids", "rev", "prev", "v", "neg", "p", "ch", "d", "r", "joinPieces", "rows", "byPath", "row", "list", "runs", "pieces", "b", "from", "i", "decodeRun", "sum", "walkCut", "nodes", "onWindow", "node", "kept", "id", "spans", "run", "first", "last", "length", "fragments", "hapStart", "hapEnd", "formatWalk", "sample", "haplotype", "contig", "steps", "tabs", "out", "WalkGraph", "window", "t", "rank", "refName", "end", "endpoint", "held", "x", "y", "seen", "links", "a", "source", "target", "to", "stepBudgetError", "budget", "filtered", "total", "perChunk", "walks", "windowBp", "read", "fitsBp", "cs", "fewerFit", "error", "NodeLimitError", "byteBudgetError", "bytesTo", "bytes", "least", "megabytes", "offReference", "segments", "segment", "checkRange", "refName", "start", "end", "getLines", "file", "opts", "WALK_CONTEXT", "RgfaTabixAdapter", "config", "getSubAdapter", "pluginManager", "walks", "header", "walkHeader", "slot", "chunk", "lookbackChunks", "under", "openTabixSlot", "walksLocation", "hasWalks", "PanSNRefNames", "lookback", "chunkQueryStart", "haplotypes", "tier", "query", "signal", "statusCallback", "observer", "tabixRefName", "line", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "index", "links", "addLinksOver", "reached", "link", "parseLinkLine", "linkKey", "layout", "row", "found", "cut", "anchoredCut", "formatSubgraph", "frontier", "hop", "spans", "closingSpans", "span", "closingLinks", "budget", "keep", "walkNameFilter", "lane", "resolvePanSNPrefix", "panSNHaplotype", "from", "files", "tooLarge", "byteBudgetError", "sum", "bytes", "reads", "stop", "rows", "graph", "WalkGraph", "read", "lineCallback", "walkRowName", "parseWalkRow", "error", "stepBudgetError", "kept", "fragments", "walkCut", "joinPieces"]
+}

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

@@ -4,5 +4,5 @@ import{a as K,b as Bn,c as Ra,d as Sa,e as Ze,f as Ht,g as $t}from"./chunks/chun
 `)&&(e.hoveredRowWalks=t)},setHoveredWalkRow(t){e.hoveredWalkRow=t},setHoveredBubble(t){e.hoveredBubble=t},setPointerInPane(t){e.pointerInPane=t},setWalkStrip(t){e.walkStrip=t,e.stripHover=null},setStripHover(t){e.stripHover=t;let n=e.walkStripRows,r=e.walkStripFrame,o=t&&n?[n.reference,...n.rows].find(i=>i.name===t.row):void 0,a=o&&r&&e.graph?Oo(e.graph,o,t.offset,r.scaleX):void 0;e.hoveredNode=a??null},setLegendSize(t){e.legendSize=t},setHoveredEdge(t){e.hoveredEdge=t},setSelectedNode(t){e.selectedNode=t},setDraggingNode(t){e.draggingNode=t},setPanning(t){e.isPanning=t},stopDragging(){e.draggingNode=null,e.isPanning=!1},clearInteractionState(){e.hoveredNode=null,e.hoveredWalkRow=null,e.hoveredBubble=null,e.hoveredEdge=null,e.selectedNode=null,e.draggingNode=null,e.isPanning=!1},showNodeDetails(t){let n=e.nodeById?.get(t),r=e.nodeById,o=e.nodeNeighbors;if(n&&r&&o){let a=(0,lt.getSession)(e),i=e.graphRegion,s=i?be({nodeId:t,nodeById:r,neighbors:o}):void 0;(0,lt.isSessionModelWithWidgets)(a)&&a.showWidget(a.addWidget("BaseFeatureWidget","baseFeature",{featureData:{id:n.id,name:n.name,length:n.length,depth:n.depth,rank:n.stable?.rank,stableName:n.stable?.refName,contributingAssembly:Ke(n)?.sample,contributingHaplotype:Ke(n)?.haplotype,sampleCount:n.samples?.length,samples:n.samples,...i&&s?{refName:i.refName,assemblyName:i.assemblyName,start:s.start,end:s.end}:{}}}))}},setTransform(t,n,r){let{host:o}=e;e.viewportOwner==="host"&&o?o.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=xn(t),e.translateX=n),e.translateY=r,e.keepDrawingInView()},zoom(t,n,r){let{host:o}=e;if(e.viewportOwner==="host"&&o){o.zoomTo(o.bpPerPx/t,n);return}e.viewportOwner="user";let a=no(e,t,n,r,e.pixelRows);e.scale=a.scale,e.translateX=a.translateX,e.translateY=a.translateY,e.keepDrawingInView()},setViewportDirty(){e.viewportRebuildPending=!1,e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){if(e.viewportOwner==="host"){let n=e.layoutBounds,r=e.facetGrid!==void 0,o=r?ee:W,a=r?ee:e.fitPadTop,i=e.viewBox.height-a-o;n&&i>0&&(e.translateY=Ln(n,i,e.scaleY,a));return}let t=e.fittedTransform;t&&(e.scale=t.scale,e.translateX=t.translateX,e.translateY=t.translateY)},clearPerfMetrics(){e.lastFetchMs=void 0,e.lastLayoutMs=void 0,e.lastGeometryMs=void 0,e.lastGeometryStrokeCount=void 0,e.builtViewport=void 0}})).actions(e=>({hostTransform(t,n){let r=e.viewportOwner!=="host";r&&(e.viewportOwner="host"),e.scale=t,e.translateX=n,r&&e.zoomToFit()},followNewLayout(t){let n=e.layoutBounds;if(e.viewportOwner!=="user"||!n||t===e.layoutResult)return;let r=t?.referenceAxis===!0&&e.xIsReferenceBp;t===void 0||r&&(!e.paneMeasured||Wi(n,e,e.viewBox))?e.keepDrawingInView():(e.viewportOwner="fit",e.zoomToFit())},refitView(){e.viewportOwner==="user"&&(e.viewportOwner="fit"),e.zoomToFit()},releaseHost(){e.viewportOwner==="host"&&(e.xIsReferenceBp?e.viewportOwner="user":(e.viewportOwner="fit",e.zoomToFit()))}})).actions(e=>{function t(){clearTimeout(e.viewportDirtyTimer),e.viewportRebuildPending=!0,e.viewportDirtyTimer=setTimeout(()=>{(0,cr.isAlive)(e)&&e.setViewportDirty()},Mo)}function n(){cancelAnimationFrame(e.positionsDirtyFrame),e.positionsDirtyFrame=requestAnimationFrame(()=>{(0,cr.isAlive)(e)&&e.setPositionsDirty()})}return{moveNode(r,o,a){let i=e.layoutResult?.nodePositions;if(i?.[r]){for(let s of i[r])s.x+=o,s.y+=a;n()}},scheduleViewportDirty:t}});var Xi=ji.actions(e=>{let t,n;function r(u){let{rpcManager:h}=(0,U.getSession)(e);return h.call((0,U.getRpcSessionId)(e),"GraphComputeLayout",{...u,signal:t?.signal,statusCallback:S=>{e.setStatusMessage((0,U.statusMessageText)(S)??"")}})}function o(){return Sn({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges})}function*a(u){let h=performance.now(),S=Ge.has(e.chosenLayoutMode),L=e.graphRegion,G=S&&L?ni(u,L):u,N=S&&e.tubeMapFold>0&&!G.reads?oi(G,e.tubeMapFold):void 0,v=O(e.chosenLayoutMode).run(N?.graph??G,e.graphRegion,e.host?e.layoutResult?.sampleRows:void 0);if(v)return{result:N&&v.tubeMap?{...v,tubeMap:{...v.tubeMap,coarse:N}}:v,duration:performance.now()-h};let D=o(),b=Ue.ready(u,D);return b?{result:b,duration:performance.now()-h}:yield Ue.layout(u,D,r)}let i=0,s,c,d=new Map;function*f(u){let h=++i,S=()=>e.graph===u&&h===i,L=t?.signal,G;try{if(e.modeDrawsNodes&&u.nodes.length>e.maxGraphNodes)throw new Error(`Graph too large to draw: ${u.nodes.length.toLocaleString()} nodes (limit ${e.maxGraphNodes.toLocaleString()}). Pick Layout \u2192 Walk rows, zoom in to a smaller region, or raise the node limit in Settings.`);G=yield*a(u)}catch(v){if(!S()||L?.aborted)return!1;throw s=v,v}let N=S();if(N){s!==void 0&&e.error===s&&(e.error=void 0),s=void 0;let v=e.layoutResult;c=u,e.layoutResult=G.result,e.setLayoutMs(G.duration),e.followNewLayout(v)}return N}function w(u,h){let S=u.anchorPaths;return u.anchoredBy==="paths"&&S?(un(u,e.assemblySpellings(h.assemblyName))??fn(S,h.assemblyName))?.name:void 0}function*p(u,h,S,L=!1,G){let N=t?.signal;e.setStatusMessage("Parsing GFA");let v=kn(u,h,{referencePath:e.referencePath||S?.assemblyName}),D=S?w(v,S):void 0,b=!e.referencePath&&D!==void 0&&D!==v.referencePath?$e(v,D):v;if(G){e.setStatusMessage("Reading alignments");try{let{records:x,total:P}=yield G(b);b.reads=x,e.readsShown={shown:x.length,total:P}}catch(x){if(N?.aborted)return;console.warn("[GraphGenomeView] no reads for this graph",x),e.readsShown=void 0}if(N?.aborted)return}else e.readsShown=void 0;let C=L?e.selectedNode:null;e.graph=b,e.graphRegion=S,e.loadedReferencePath=D,e.indexBubbles=void 0,e.geneTrackFeatures=void 0,e.walkGeneFeatures=void 0,d.clear(),e.repeatArrays=void 0,e.popStack=[],e.clearInteractionState(),C!==null&&b.nodes.some(x=>x.id===C)&&(e.selectedNode=C),e.setStatusMessage("Computing layout"),yield*f(b)}let l=0,R;function M(){let u=++l;return t?.abort(),t=new AbortController,R=u,e.loadCanceled=!1,{isLive:()=>u===l,signal:t.signal}}function A(){R=void 0,e.finishLoading()}function g(){R===void 0&&e.finishLoading()}function*k(u,h,S,L){let G=xo(u);if(!(u.type!=="RgfaTabixAdapter"||G===void 0))try{let N=yield(0,U.getSession)(e).rpcManager.call((0,U.getRpcSessionId)(e),"CoreGetFeatures",{adapterConfig:{type:"MinigraphBubbleAdapter",uri:`${G}.bubbles.bed.gz`,baseUri:u.baseUri,assemblyNameToPanSN:u.assemblyNameToPanSN},regions:[h],signal:L});if(S()){let v=N.map(C=>({refName:h.refName,start:C.get("start"),end:C.get("end"),segmentCount:C.get("segmentCount"),pathCount:C.get("pathCount")??0,inversion:C.get("inversion"),shortestAlleleLength:C.get("shortestAlleleLength"),longestAlleleLength:C.get("longestAlleleLength"),segments:C.get("segments"),shortestAllele:void 0,longestAllele:void 0})),[D,...b]=e.popStack;D?e.popStack=[{...D,indexBubbles:v},...b]:e.indexBubbles=v}}catch(N){console.warn("[GraphGenomeView] no bubble index for this graph",N)}}function*T(u,h,S,L){let G=(0,U.getSession)(e),N=u?G.tracks.find(v=>v.trackId===u):void 0;if(N)try{return yield G.rpcManager.call((0,U.getRpcSessionId)(e),"CoreGetFeatures",{adapterConfig:(0,zi.readConfObject)(N,"adapter"),regions:[h],signal:L})}catch(v){console.warn(`[GraphGenomeView] no ${S} for this graph`,v);return}}function*B(u,h,S){let L=yield*T(e.geneTrack?.trackId,u,"genes",S);L&&h()&&(e.geneTrackFeatures=L)}function*V(u,h,S){let L=yield*T(e.repeatTrack?.trackId,u,"repeats",S);L&&h()&&(e.repeatArrays=Ti(L))}function*y(u,h,S){let{isLive:L,signal:G}=M();e.isLoading=!0,e.error=void 0;try{let N=typeof h=="string"?h:yield h(G);L()&&(yield*p(N,u,S))}catch(N){L()&&(console.error("[GraphGenomeView.loadWholeGFA]",N),e.error=N)}finally{L()&&A()}return L()}function I(){t?.abort(),t=void 0,R=void 0,l++,i++}function E(){I(),e.graph=void 0,e.graphRegion=void 0,e.loadedReferencePath=void 0,e.layoutResult=void 0,e.indexBubbles=void 0,e.geneTrackFeatures=void 0,e.walkGeneFeatures=void 0,d.clear(),e.repeatArrays=void 0,e.readsShown=void 0,e.popStack=[],e.error=void 0,e.isLoading=!1,e.loadCanceled=!1,e.statusMessage="",e.clearInteractionState(),e.clearPerfMetrics(),e.viewportOwner==="user"&&(e.viewportOwner="fit")}return{clearGraph(){E()},cancelLoad(){e.canCancelLoad&&(E(),e.loadCanceled=!0)},stopLoad(){I(),e.graph!==c&&(e.layoutResult=void 0),e.isLoading=!1,e.statusMessage="",e.loadCanceled=!0},beforeDestroy(){I()},loadGFA:(0,_.flow)(function*(u,h="Imported GFA"){yield*y(h,u)}),loadGFAFromLocation:(0,_.flow)(function*(u,h){e.setStatusMessage("Fetching GFA");let S=yield*y(Ye(u)||"GFA",L=>(0,dr.openLocation)(u).readFile({encoding:"utf8",signal:L}),h);if(h&&S&&e.graph){let L=()=>e.graphRegion===h;yield Promise.all([(0,_.flow)(B)(h,L),(0,_.flow)(V)(h,L)])}}),cutSubgraph:(0,_.flow)(function*(u,h,S={}){let{isLive:L,signal:G}=M();e.isLoading=!0,e.error=void 0,e.setStatusMessage("Fetching subgraph");try{let N=performance.now(),v=yield(0,U.getSession)(e).rpcManager.call((0,U.getRpcSessionId)(e),"GetSubgraph",{adapterConfig:u,region:h,opts:S,signal:G});if(!L())return;if(e.setFetchMs(performance.now()-N),!v)throw new Error("Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph");if(yield*p(v,Je(h),h,!0,Fa(u)?D=>(0,U.getSession)(e).rpcManager.call((0,U.getRpcSessionId)(e),"GetGraphReads",{adapterConfig:u,nodeNames:D.nodes.map(b=>b.name),signal:G}):void 0),!L())return;e.setStatusMessage("Reading annotations"),yield Promise.all([S.tier==="coarse"?void 0:(0,_.flow)(k)(u,h,L,G),(0,_.flow)(B)(h,L,G),(0,_.flow)(V)(h,L,G)])}catch(N){L()&&(console.error("[GraphGenomeView.cutSubgraph]",N),e.error=N)}finally{L()&&A()}}),reloadRepeats:(0,_.flow)(function*(){let u=e.graphRegion,h=e.repeatTrack?.trackId;u&&(e.repeatArrays=void 0,yield*V(u,()=>e.graphRegion===u&&e.repeatTrack?.trackId===h))}),loadWalkRowSampleTable:(0,_.flow)(function*(){let u=e.walkRowSamplesTsv,h=u?JSON.stringify(u):void 0;if(h!==n&&(n=h,e.walkRowSampleTable=void 0,!!u))try{let S=yield(0,dr.openLocation)(u).readFile("utf8");(0,_.isAlive)(e)&&h===n&&(e.walkRowSampleTable=oo(S))}catch(S){(0,_.isAlive)(e)&&h===n&&(0,U.getSession)(e).notify(`Walk rows cannot be grouped: the samples table did not load (${String(S)})`,"warning")}}),loadWalkGenes:(0,_.flow)(function*(){let u=e.walkGeneReads?.reads??[],h=JSON.stringify(u),S=e.graph,L=new Map;yield Promise.all(u.map(({row:G,trackId:N,region:v})=>(0,_.flow)(function*(){let D=`${N} ${v.refName}:${v.start}-${v.end}`,b=d.get(D);if(!b){let C=yield*T(N,v,"haplotype genes");if(!C)return;b=qt(C).map(x=>({...x,refName:v.refName})),d.set(D,b)}L.set(G,b)})())),(0,_.isAlive)(e)&&e.graph===S&&JSON.stringify(e.walkGeneReads?.reads??[])===h&&(e.walkGeneFeatures=u.length?L:void 0)}),reloadGenes:(0,_.flow)(function*(){d.clear();let u=e.graphRegion,h=e.geneTrack?.trackId;u&&(e.geneTrackFeatures=void 0,yield*B(u,()=>e.graphRegion===u&&e.geneTrack?.trackId===h))}),popBubble:(0,_.flow)(function*(u){let h=e.graph;if(!h)return;let S=$n(h,Et(u));if(S.nodes.length===0){(0,U.getSession)(e).notify("None of the segments of this bubble are in the cut; widen the graph context to open it","info");return}e.popStack=[...e.popStack,{graph:h,layoutMode:e.layoutMode,label:h.name,indexBubbles:e.indexBubbles}],e.indexBubbles=void 0;let L=`${Co[Bt(u,e.repeatArrays).kind]} at ${u.refName}:${u.start.toLocaleString()}`;e.graph={...S,name:L},e.clearInteractionState(),e.viewportOwner="fit",e.isLoading=!0;try{(yield*f(e.graph))&&g()}catch(G){e.error=G,g()}}),unpopBubble:(0,_.flow)(function*(){let u=e.poppedFrom;if(u){e.popStack=e.popStack.slice(0,-1),e.graph=u.graph,e.layoutMode=u.layoutMode,e.indexBubbles=u.indexBubbles,e.clearInteractionState(),e.viewportOwner="fit",e.isLoading=!0;try{(yield*f(u.graph))&&g()}catch(h){e.error=h,g()}}}),recomputeLayout:(0,_.flow)(function*(){let u=e.graph;if(u){e.isLoading=!0,e.setStatusMessage("Computing layout");try{(yield*f(u))&&g()}catch(h){console.error("[GraphGenomeView.recomputeLayout]",h),e.error=h,g()}}})}});function rd(e){return q(e)&&typeof e.get=="function"}function od(e){let t=rd(e)?e.get("name"):q(e)?e.name:void 0;return typeof t=="string"?t:void 0}function Yi(e){let t;if(q(e)&&q(e.hoverPosition)){let{refName:n,coord:r,coord0:o,assemblyName:a}=e.hoverPosition;typeof n=="string"&&typeof r=="number"&&(t={refName:n,coord:typeof o=="number"?o:r-1,assemblyName:typeof a=="string"?a:void 0,featureName:od(e.hoverFeature)})}return t}function Ui(e,t){return(e.assemblyName===void 0||e.assemblyName===t.assemblyName)&&e.refName===t.refName&&e.coord>=t.start&&e.coord<t.end}function Ki({hover:e,nodes:t}){let n,r;for(let o of t)o.name===e.featureName?n=o.id:r===void 0&&Z(o)&&e.coord>=o.stable.start&&e.coord<o.stable.start+o.length&&(r=o.id);return n??r??null}var ad=/^(.+) HP(\d+)$/,id=/^(.+)\.(\d+)$/;function sd(e){let t=ad.exec(e),n=id.exec(e);return[...t?[{sample:t[1],haplotype:String(Number(t[2])+1)}]:[],...n?[{sample:n[1],haplotype:n[2]}]:[],{sample:e,haplotype:void 0}]}function cd(e){return Q(e).name.split("#")[1]}function qi(e,t){let n=t.map(r=>r.name);for(let{sample:r,haplotype:o}of sd(e)){let a=n.filter(i=>Tr(Q(i).name)===r&&(o===void 0||cd(i)===o));if(a.length>0)return a}return[]}var Zi=Xi.actions(e=>({startRenderingBackend(t){if(!e.autorunsInstalled){(0,ie.addDisposer)(e,(0,z.autorun)(()=>{e.fittedTransform&&(0,z.untracked)(()=>e.viewportOwner==="fit")&&e.zoomToFit()})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>`${e.viewBox.width} ${e.viewBox.height}`,()=>{e.keepDrawingInView()})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>{let r=e.facetGrid;return r?`${e.facet.field} ${e.facetPanels?.length} ${r.columns}`:""},()=>{e.refitView()})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>({graph:e.graph,reads:JSON.stringify(e.walkGeneReads?.reads??[])}),()=>{e.loadWalkGenes()},{fireImmediately:!0,equals:(r,o)=>r.graph===o.graph&&r.reads===o.reads})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>e.chosenLayoutMode==="walkrows"?JSON.stringify(e.walkRowSamplesTsv??null):void 0,r=>{r!==void 0&&e.loadWalkRowSampleTable()},{fireImmediately:!0})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>e.fitPadTop,()=>{e.viewportOwner==="host"&&e.zoomToFit()})),(0,ie.addDisposer)(e,(0,z.autorun)(()=>{let r=Yi((0,Ji.getSession)(e).hovered);(0,z.untracked)(()=>{let o=e.graphRegion,a=e.graph,i=r&&o&&Ui(r,o)?r:void 0,s=i?.featureName&&a?.paths?qi(i.featureName,a.paths):[];o&&a&&!e.pointerInPane&&e.setHoveredNode(i&&s.length===0?Ki({hover:i,nodes:a.nodes}):null),e.setHoveredRowWalks(s)})})),(0,ie.addDisposer)(e,(0,z.reaction)(()=>`${e.scale}-${e.translateX}-${e.translateY}`,()=>{e.setHoveredNode(null),e.setHoveredBubble(null),e.setHoveredEdge(null)},{name:"GraphClearHoverOnViewportChange"}));let n=!0;(0,ie.addDisposer)(e,(0,z.autorun)(()=>{let{scale:r}=e,o=Ct(e);if(n){n=!1;return}let a=(0,z.untracked)(()=>e.builtViewport);a?.scale===r&&to(a.bounds,o)||e.scheduleViewportDirty()})),(0,ie.addDisposer)(e,(0,z.autorun)(()=>{let r=e.currentRenderingBackend;he(e.geometryVersion),r&&(e.applyHighlights(r),e.renderNow())}))}e.attachRenderingBackend(t,()=>({upload:n=>{if(n.resize(e.paneWidth,e.canvasHeight),e.layoutResult?.tubeMap||e.facetPanels)return he(e.viewportDirty),n.uploadGeometry(To),e.setGeometryMetrics(0,0,{scale:(0,z.untracked)(()=>e.scale),bounds:(0,z.untracked)(()=>e.viewportToBuild())}),!0;let r=performance.now(),o=e.buildDrawing(e.walkLift,e.effectiveDrawPaths);return o?(n.uploadGeometry(o.batch),e.setGeometryMetrics(performance.now()-r,o.batch.nodeStrokes.length,{scale:(0,z.untracked)(()=>e.scale),bounds:o.viewportBounds}),!0):!1},render:n=>e.nodePositions?(e.paint(n),e.markPainted(),!0):!1,releaseTargets:n=>{n.releaseOffscreenTargets()}}))}})).actions(e=>({switchLayout(t){return e.setLayoutMode(t),e.recomputeLayout()},toggleDeletionEdges(){return e.setShowDeletionEdges(!e.showDeletionEdges),e.usesLayoutEngine?e.recomputeLayout():void 0},retryLoad(){},afterAttach(){e.isDefaultViewport||(e.viewportOwner="user")}}));var en=m(K(),1);var dd="FeatureTrack";function Qi({session:e,assemblyName:t,first:n}){let r=fe(e,t),o=[];for(let a of e.tracks){let i=(0,en.readConfObject)(a,"type"),s=(0,en.readConfObject)(a,"assemblyNames"),c=(0,en.readConfObject)(a,"trackId");i===dd&&Array.isArray(s)&&s.some(d=>typeof d=="string"&&fe(e,d)===r)&&typeof c=="string"&&c!==n&&o.push(c)}return n?[n,...o]:o}var tn=m(K(),1),es=m(oc(),1),nn=m(ae(),1);var pd="SyntenyTrack",ud="Synteny adapters";function md(e){if((0,tn.readConfObject)(e,"type")===pd)return!0;let t=e.adapter?.type;if(typeof t!="string"||!(0,nn.isStateTreeNode)(e))return!1;let{pluginManager:n}=(0,nn.getEnv)(e);return!!n?.hasAdapterType(t)&&n.getAdapterType(t).adapterMetadata?.category===ud}function ts(e,t){let n=new Set(t),r=[];for(let o of e.tracks){let a=(0,tn.readConfObject)(o,"assemblyNames"),i=(0,tn.readConfObject)(o,"trackId");if(md(o)&&typeof i=="string"&&Array.isArray(a)){let s=a.filter(c=>typeof c=="string"&&n.has(fe(e,c))).length;s>=2&&r.push({trackId:i,name:(0,es.getTrackName)(o,e),coverage:s})}}return r.sort((o,a)=>a.coverage-o.coverage)}function ns(e,t,n="image/svg+xml"){let r=URL.createObjectURL(new Blob([e],{type:n})),o=document.createElement("a");o.href=r,o.download=t,o.click(),setTimeout(()=>{URL.revokeObjectURL(r)},0)}var os=Zi.actions(e=>({showInLinearView(t){let n=(0,ge.getSession)(e),r=t.assembly===e.graphRegion?.assemblyName,o=Ci({session:n,location:t.location,assembly:t.assembly,connectedViewId:e.connectedViewId,tracks:Qi({session:n,assemblyName:t.assembly,first:r?e.sourceTrackId:void 0})});r&&e.pairWithLinearView(o)},highlightInLinearView(t){Bi({session:(0,ge.getSession)(e),location:t.location,assembly:t.assembly,connectedViewId:e.connectedViewId})},showSyntenyView(t){Ei({session:(0,ge.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?ts((0,ge.getSession)(e),t):[]}})).views(e=>({walkRowSampleMenuItems(){let{disagreeing:t}=e.walkRowSampleChoices,n=e.walkRowSamples,r=o=>o.join(`
 `)===n?.join(`
 `);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:r(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:n!==void 0&&!r(t),onClick:()=>{(0,ge.getSession)(e).queueDialog(o=>[yo,{model:e,onClose:o}])}}]},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({repeat:t=!0}={}){return[...Ge.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:So.map(({bp:n,label:r})=>({type:"radio",label:r,checked:e.tubeMapFold===n,disabled:n>0&&e.graph?.reads!==void 0,onClick:()=>{e.setTubeMapFold(n),e.recomputeLayout()}}))}]:[],...t&&e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:[{type:"radio",label:"Whole window",checked:!e.selectedRepeat,onClick:()=>{e.setRepeatKey("")}},...e.repeatChoices.map(({key:n,name:r,unit:o})=>({type:"radio",label:`${r} \xB7 ${o.toLocaleString()} bp unit`,checked:e.repeatKey===n,onClick:()=>{e.setRepeatKey(n)}}))]}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){return[{type:"checkbox",label:"Show bubble halos",checked:e.showBubbles,onClick:()=>{e.setShowBubbles(!e.showBubbles)}},{type:"checkbox",label:"Show deletion edges",checked:e.showDeletionEdges,onClick:()=>{e.toggleDeletionEdges()}},{type:"checkbox",label:"Show hover highlight",checked:e.chosenHighlightOnHover,onClick:()=>{e.setHighlightOnHover(!e.chosenHighlightOnHover)}},{type:"checkbox",label:"Show genes on the backbone",checked:e.showGenes,onClick:()=>{e.setShowGenes(!e.showGenes)}},...e.referenceStripApplies?[{type:"checkbox",label:"Show reference strip",checked:e.showReferenceStrip,onClick:()=>{e.setShowReferenceStrip(!e.showReferenceStrip)}}]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:ti,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&ns(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}},{label:"Copy figure spec",icon:qa,disabled:e.figureSpecUnavailable!==void 0,disabledHelpText:e.figureSpecUnavailable,onClick:()=>{let t=e.figureSpec(),n=(0,ge.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(r=>{n.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let n=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),o=n.length>Ro;return[{type:"subHeader",label:"Highlight"},...o?[{label:"Choose haplotypes...",onClick:()=>{(0,ge.getSession)(e).queueDialog(a=>[wo,{model:e,onClose:a}])}}]:[],...(o?n.filter(a=>r(a.name)):n).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{(0,ge.getSession)(e).queueDialog(a=>[ko,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...Jr.map(({value:a,label:i})=>({type:"radio",label:a==="walk"?"A panel per haplotype":i,checked:e.facet.field===a,onClick:()=>{e.setFacet(a)}}))]:[]]},colorSchemeLabel(t){let n=yn.find(r=>r.value===t)?.label??t;return t==="auto"?`${n} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:n},graphMenuItems(){let t=this.layoutOptionMenuItems();return[{label:`Layout: ${O(e.chosenLayoutMode).label.replace(/ layout$/,"")}`,icon:Za,subMenu:[...Yr.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description,onClick:()=>{e.switchLayout(n.value)}})),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${this.colorSchemeLabel(e.chosenColorScheme)}`,icon:ei,subMenu:yn.map(n=>({type:"radio",label:this.colorSchemeLabel(n.value),checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},{label:"Show...",icon:Qr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let n of ka({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:r=>{e.showInLinearView(r)},onShowSynteny:r=>{e.showSyntenyView(r)}}))(0,rs.pushLaunchViewMenuItem)(t,n);return t}}));function rn(){return os}function pr(){return Y.types.compose("GraphGenomeView",as.BaseViewModel,rn(),Y.types.model({type:Y.types.literal("GraphGenomeView"),gfaLocation:Y.types.maybe(Y.types.frozen()),loadedRegion:Y.types.maybe(Y.types.frozen()),loadedTrackId:Y.types.optional(Y.types.string,""),subgraphContext:Y.types.optional(Y.types.number,1),subgraphHaplotypes:Y.types.maybe(Y.types.frozen()),maxRegionBp:Y.types.optional(Y.types.number,Xe)})).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(){let t=this.sourceTrack;return e.subgraphHaplotypes??(t?Ze(le(e,t)):void 0)},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,is.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(Ye(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let r=e.sourceTrack,o=n.end-n.start,a=r?$t(Ht(r),n.assemblyName):void 0;if(!r)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(o>e.maxRegionBp)e.setError(new Error(`Region too large (${ye(o)}) \u2014 zoom in to view graph (max ${ye(e.maxRegionBp)})`));else return e.cutSubgraph(le(e,r),n,{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...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,Y.addDisposer)(e,(0,ss.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!O(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ld=(0,ps.defineLaunchKeys)()({});function ur(e){e.addViewType(()=>new ds.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:pr(),launchKeys:ld,ReactComponent:(0,cs.lazy)(()=>import("./chunks/GraphGenomeView-WPF4JRXE.js"))}))}var us=m(K(),1),Pe=m(me(),1),mr=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function gd(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...mr.map(o=>r(n(o)))].filter(o=>o!==void 0)}function lr(e){e.addTrackType(()=>{let t=(0,us.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Pe.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Pe.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Pe.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of gd(e))n.addDisplayType(r);return n})}function gr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Cs=m(wt(),1),Bs=m(ls(),1);var fs=m(K(),1),bs=m(hs(),1),hr=m(ae(),1);function ys(){return(0,fs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:hr.types.enumeration("LayoutMode",Ur),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:hr.types.enumeration("ColorScheme",qr),defaultValue:"auto"},highlightOnHover:{type:"boolean",defaultValue:!0},...(0,bs.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Ts=m(wt(),1);var Ce=m(K(),1),Gs=m(me(),1),Ns=m(ks(),1),As=m(Fr(),1),Be=m(ne(),1),Ps=m(Ss(),1),F=m(ae(),1),on=m(Ls(),1);var Ie=m(yt(),1);function Ms(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 vs(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 hd=(0,Ts.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-H4QX5DAF.js"));function Is(e){return F.types.compose("LinearGraphDisplay",Gs.BaseDisplay,(0,Ps.default)(),rn(),F.types.model({type:F.types.literal("LinearGraphDisplay"),configuration:(0,Ce.ConfigurationReference)(e),pane:F.types.maybe(F.types.frozen()),overviewRowsChoice:F.types.maybe(F.types.frozen()),overviewRowOrder:F.types.maybe(F.types.frozen()),cutRegion:F.types.maybe(F.types.frozen()),coarseCut:F.types.optional(F.types.boolean,!1),maxRegionBp:F.types.optional(F.types.number,Xe),subgraphContext:F.types.optional(F.types.number,1),subgraphHaplotypes:F.types.maybe(F.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:r,overviewRowOrder:o,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0})).views(t=>({get adapterConfig(){return le(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,Ce.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,Ce.getConf)(t,"colorScheme")},get defaultHighlightOnHover(){return(0,Ce.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??Ze(this.adapterConfig)??Bn(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${ye(n.end-n.start)}, max ${ye(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return(0,Ns.computeSvgReady)({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return(0,on.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,on.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n,t.dense=void 0},setDense(n){t.dense=n},setHaplotypeNames(n){t.haplotypeNames=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=$t(Ht(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0,...O(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Un(n,t.capFor(r),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=O(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||vs(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&bi(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,F.isAlive)(t)&&Ms(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=O(t.chosenLayoutMode);t.setLayoutMode(n);let o=O(n),a=t.host?Yt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(n){try{let r=await(0,Be.getSession)(t).rpcManager.call((0,Be.getRpcSessionId)(t),"GetGraphHaplotypes",{adapterConfig:n});(0,F.isAlive)(t)&&t.setHaplotypeNames(r)}catch(r){console.warn("[LinearGraphDisplay] no haplotype names",r)}}})).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,F.addDisposer)(t,(0,Ie.reaction)(()=>Ra(t.adapterConfig)?t.adapterConfig:void 0,n=>{t.setHaplotypeNames(void 0),n&&t.fetchHaplotypeNames(n)},{fireImmediately:!0,name:"GraphHaplotypeNames"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Yt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Yt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,F.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Be.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({cutMenuItems(){if(!Sa(t.adapterConfig))return[];let n=Ze(t.adapterConfig),r=Bn(t.parentTrack.configuration),o=t.haplotypeNames,a=t.subgraphHaplotypes,i=s=>{t.setSubgraphHaplotypes(s),t.cut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:o?`Every haplotype in the graph (${o.length.toLocaleString()})`:"Every haplotype in the graph",checked:a?a.length===0:!n&&!r,onClick:()=>{i([])}},...n||r?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${r?.length} assemblies`,checked:a===void 0,onClick:()=>{i(void 0)}}]:[],{type:"radio",label:"Chosen in Settings...",checked:(a?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){(0,Be.getSession)(t).queueDialog(n=>[hd,{model:t,open:!0,onClose:n}])},async renderSvg(n){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-35VDH2K7.js");return r(t,n)},trackMenuItems(){let n=t.launchMenuItems();(0,As.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:_t,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:xa,subMenu:r}]:[],...t.graphMenuItems(),{label:"Settings",icon:La,onClick:()=>{this.openSettings()}},...n]}}))}function fr(e){e.addDisplayType(()=>{let t=ys();return Object.assign(new Bs.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Is(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Cs.lazy)(()=>import("./chunks/LinearGraphDisplay-ZJNR2KCT.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Ds=m(Wt(),1);var br=m(K(),1),Es=m(ae(),1);function yr(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var fd=(0,br.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,br.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Es.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:yr}),Fs=fd;function wr(e){e.addAdapterType(()=>new Ds.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:yr,configSchema:Fs,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-PP3LVTLY.js").then(t=>t.default)}))}var Os=m(Wt(),1);var an=m(K(),1),Hs=m(ae(),1);function gt(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Vs(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:gt(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:gt(`${t}.links.bed.gz`,n,r)}:e}function bd(e){let{walksUri:t,baseUri:n,csi:r}=e;if(typeof t!="string")return e;let o=a=>`${t}.${a}.bed.gz`;return{...e,walksLocation:{uri:o("walks"),baseUri:n},walksIndex:gt(o("walks"),n,r),segmentsLocation:{uri:o("nodes"),baseUri:n},segmentsIndex:gt(o("nodes"),n,r),linksLocation:{uri:o("links"),baseUri:n},linksIndex:gt(o("links"),n,r)}}function kr(e){let{coarse:t,baseUri:n,csi:r}=e;return bd(Vs(typeof t=="object"&&t!==null?{...e,coarse:Vs({baseUri:n,csi:r,...t})}:e))}var ht=(e,t)=>(0,an.ConfigurationSchema)(e,{indexType:{model:Hs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),yd=(0,an.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ht("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:ht("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wd=(0,an.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ht("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:ht("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}},walksIndex:ht("RgfaWalksIndex",""),walkChunk:{type:"integer",defaultValue:65536},walkStepBudget:{type:"integer",defaultValue:4e6},walkByteBudget:{type:"integer",defaultValue:8e6},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:yd},{explicitlyTyped:!0,preProcessSnapshot:kr}),$s=wd;function Rr(e){e.addAdapterType(()=>new Os.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:kr,configSchema:$s,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-2CIFHOB3.js").then(t=>t.default)}))}var kd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Rd(e){return Er(e).toLowerCase().endsWith(".gbz.db")}function Sd(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 xd(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Rd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Dr(e))return Vr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Sr(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Sd),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>xd(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>kd.has(n)?"GraphTrack":t(n,r))}var zs=m(ne(),1),sn=m(ic(),1),xr=m(ac(),1),Xs=m(sc(),1);function _s(e){let t;if(q(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Ld(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Ws(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Md(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>q(n)&&Array.isArray(n.displays)?n.displays.filter(r=>q(r)&&r.type==="LinearGraphDisplay"):[])}function js(e,t,n){let r=[],o=ut(e),a=new Set(o.map(i=>q(i)?i.id:void 0));for(let i of o){if(q(i)&&i.id===t)for(let s of Md(i)){let c=_s(s.hoverHighlight);c&&Ws(c,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(q(i)&&i.type==="GraphGenomeView"&&Ld(i,t,a)){let s=_s(i.hoverHighlight);s&&Ws(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ee=m(ue(),1),vd=(0,Xs.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,sn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,sn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,sn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Td=(0,xr.observer)(function({model:t,region:n}){let{classes:r}=vd(),o=t.getHighlightCoords(n);return o?(0,Ee.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Gd=(0,xr.observer)(function({model:t}){let{views:n}=(0,zs.getSession)(t);return(0,Ee.jsx)(Ee.Fragment,{children:js([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Ee.jsx)(Td,{model:t,region:o},`graph-hover-${r}`))})}),Ys=Gd;var Us=m(ue(),1),Nd="LinearGenomeView-TracksContainerComponent";function Lr(e){e.contributeToExtensionPoint(Nd,({model:t})=>(0,Us.jsx)(Ys,{model:t},"graphgenomeview-hover-highlight"))}var Ks=m(me(),1);function Ad(e){return e.views(t=>({get adapterConfig(){return le(t,t.parentTrack.configuration)}}))}function Mr(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Ks.DisplayType&&mr.includes(t.name)&&t.extendStateModel(Ad),t))}var qs="GraphGenomeView";var Js="6.9.1";var vr=class extends Zs.default{constructor(){super(...arguments);this.name=qs;this.version=Js}install(n){ur(n),fr(n),lr(n),gr(n),Lr(n),Rr(n),wr(n),Dn(n),Vn(n),Sr(n),Mr(n),n.addRpcMethod(()=>new nt(n)),n.addRpcMethod(()=>new tt(n)),n.addRpcMethod(()=>new et(n)),n.addRpcMethod(()=>new Qe(n))}configure(n){try{(0,Qs.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:_t,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{vr 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(r=>{n.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let n=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),o=n.length>Ro;return[{type:"subHeader",label:"Highlight"},...o?[{label:"Choose haplotypes...",onClick:()=>{(0,ge.getSession)(e).queueDialog(a=>[wo,{model:e,onClose:a}])}}]:[],...(o?n.filter(a=>r(a.name)):n).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{(0,ge.getSession)(e).queueDialog(a=>[ko,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...Jr.map(({value:a,label:i})=>({type:"radio",label:a==="walk"?"A panel per haplotype":i,checked:e.facet.field===a,onClick:()=>{e.setFacet(a)}}))]:[]]},colorSchemeLabel(t){let n=yn.find(r=>r.value===t)?.label??t;return t==="auto"?`${n} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:n},graphMenuItems(){let t=this.layoutOptionMenuItems();return[{label:`Layout: ${O(e.chosenLayoutMode).label.replace(/ layout$/,"")}`,icon:Za,subMenu:[...Yr.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description,onClick:()=>{e.switchLayout(n.value)}})),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${this.colorSchemeLabel(e.chosenColorScheme)}`,icon:ei,subMenu:yn.map(n=>({type:"radio",label:this.colorSchemeLabel(n.value),checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},{label:"Show...",icon:Qr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let n of ka({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:r=>{e.showInLinearView(r)},onShowSynteny:r=>{e.showSyntenyView(r)}}))(0,rs.pushLaunchViewMenuItem)(t,n);return t}}));function rn(){return os}function pr(){return Y.types.compose("GraphGenomeView",as.BaseViewModel,rn(),Y.types.model({type:Y.types.literal("GraphGenomeView"),gfaLocation:Y.types.maybe(Y.types.frozen()),loadedRegion:Y.types.maybe(Y.types.frozen()),loadedTrackId:Y.types.optional(Y.types.string,""),subgraphContext:Y.types.optional(Y.types.number,1),subgraphHaplotypes:Y.types.maybe(Y.types.frozen()),maxRegionBp:Y.types.optional(Y.types.number,Xe)})).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(){let t=this.sourceTrack;return e.subgraphHaplotypes??(t?Ze(le(e,t)):void 0)},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,is.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(Ye(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let r=e.sourceTrack,o=n.end-n.start,a=r?$t(Ht(r),n.assemblyName):void 0;if(!r)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(o>e.maxRegionBp)e.setError(new Error(`Region too large (${ye(o)}) \u2014 zoom in to view graph (max ${ye(e.maxRegionBp)})`));else return e.cutSubgraph(le(e,r),n,{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...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,Y.addDisposer)(e,(0,ss.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!O(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ld=(0,ps.defineLaunchKeys)()({});function ur(e){e.addViewType(()=>new ds.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:pr(),launchKeys:ld,ReactComponent:(0,cs.lazy)(()=>import("./chunks/GraphGenomeView-WPF4JRXE.js"))}))}var us=m(K(),1),Pe=m(me(),1),mr=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function gd(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...mr.map(o=>r(n(o)))].filter(o=>o!==void 0)}function lr(e){e.addTrackType(()=>{let t=(0,us.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Pe.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Pe.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Pe.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of gd(e))n.addDisplayType(r);return n})}function gr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Cs=m(wt(),1),Bs=m(ls(),1);var fs=m(K(),1),bs=m(hs(),1),hr=m(ae(),1);function ys(){return(0,fs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:hr.types.enumeration("LayoutMode",Ur),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:hr.types.enumeration("ColorScheme",qr),defaultValue:"auto"},highlightOnHover:{type:"boolean",defaultValue:!0},...(0,bs.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Ts=m(wt(),1);var Ce=m(K(),1),Gs=m(me(),1),Ns=m(ks(),1),As=m(Fr(),1),Be=m(ne(),1),Ps=m(Ss(),1),F=m(ae(),1),on=m(Ls(),1);var Ie=m(yt(),1);function Ms(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 vs(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 hd=(0,Ts.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-H4QX5DAF.js"));function Is(e){return F.types.compose("LinearGraphDisplay",Gs.BaseDisplay,(0,Ps.default)(),rn(),F.types.model({type:F.types.literal("LinearGraphDisplay"),configuration:(0,Ce.ConfigurationReference)(e),pane:F.types.maybe(F.types.frozen()),overviewRowsChoice:F.types.maybe(F.types.frozen()),overviewRowOrder:F.types.maybe(F.types.frozen()),cutRegion:F.types.maybe(F.types.frozen()),coarseCut:F.types.optional(F.types.boolean,!1),maxRegionBp:F.types.optional(F.types.number,Xe),subgraphContext:F.types.optional(F.types.number,1),subgraphHaplotypes:F.types.maybe(F.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:r,overviewRowOrder:o,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0})).views(t=>({get adapterConfig(){return le(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,Ce.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,Ce.getConf)(t,"colorScheme")},get defaultHighlightOnHover(){return(0,Ce.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??Ze(this.adapterConfig)??Bn(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${ye(n.end-n.start)}, max ${ye(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return(0,Ns.computeSvgReady)({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return(0,on.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,on.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n,t.dense=void 0},setDense(n){t.dense=n},setHaplotypeNames(n){t.haplotypeNames=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=$t(Ht(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0,...O(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Un(n,t.capFor(r),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=O(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||vs(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&bi(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,F.isAlive)(t)&&Ms(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=O(t.chosenLayoutMode);t.setLayoutMode(n);let o=O(n),a=t.host?Yt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(n){try{let r=await(0,Be.getSession)(t).rpcManager.call((0,Be.getRpcSessionId)(t),"GetGraphHaplotypes",{adapterConfig:n});(0,F.isAlive)(t)&&t.setHaplotypeNames(r)}catch(r){console.warn("[LinearGraphDisplay] no haplotype names",r)}}})).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,F.addDisposer)(t,(0,Ie.reaction)(()=>Ra(t.adapterConfig)?t.adapterConfig:void 0,n=>{t.setHaplotypeNames(void 0),n&&t.fetchHaplotypeNames(n)},{fireImmediately:!0,name:"GraphHaplotypeNames"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,F.addDisposer)(t,(0,Ie.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Yt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Yt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,F.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Be.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({cutMenuItems(){if(!Sa(t.adapterConfig))return[];let n=Ze(t.adapterConfig),r=Bn(t.parentTrack.configuration),o=t.haplotypeNames,a=t.subgraphHaplotypes,i=s=>{t.setSubgraphHaplotypes(s),t.cut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:o?`Every haplotype in the graph (${o.length.toLocaleString()})`:"Every haplotype in the graph",checked:a?a.length===0:!n&&!r,onClick:()=>{i([])}},...n||r?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${r?.length} assemblies`,checked:a===void 0,onClick:()=>{i(void 0)}}]:[],{type:"radio",label:"Chosen in Settings...",checked:(a?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){(0,Be.getSession)(t).queueDialog(n=>[hd,{model:t,open:!0,onClose:n}])},async renderSvg(n){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-35VDH2K7.js");return r(t,n)},trackMenuItems(){let n=t.launchMenuItems();(0,As.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:_t,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:xa,subMenu:r}]:[],...t.graphMenuItems(),{label:"Settings",icon:La,onClick:()=>{this.openSettings()}},...n]}}))}function fr(e){e.addDisplayType(()=>{let t=ys();return Object.assign(new Bs.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Is(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Cs.lazy)(()=>import("./chunks/LinearGraphDisplay-ZJNR2KCT.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Ds=m(Wt(),1);var br=m(K(),1),Es=m(ae(),1);function yr(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var fd=(0,br.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,br.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Es.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:yr}),Fs=fd;function wr(e){e.addAdapterType(()=>new Ds.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:yr,configSchema:Fs,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-PP3LVTLY.js").then(t=>t.default)}))}var Os=m(Wt(),1);var an=m(K(),1),Hs=m(ae(),1);function gt(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Vs(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:gt(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:gt(`${t}.links.bed.gz`,n,r)}:e}function bd(e){let{walksUri:t,baseUri:n,csi:r}=e;if(typeof t!="string")return e;let o=a=>`${t}.${a}.bed.gz`;return{...e,walksLocation:{uri:o("walks"),baseUri:n},walksIndex:gt(o("walks"),n,r),segmentsLocation:{uri:o("nodes"),baseUri:n},segmentsIndex:gt(o("nodes"),n,r),linksLocation:{uri:o("links"),baseUri:n},linksIndex:gt(o("links"),n,r)}}function kr(e){let{coarse:t,baseUri:n,csi:r}=e;return bd(Vs(typeof t=="object"&&t!==null?{...e,coarse:Vs({baseUri:n,csi:r,...t})}:e))}var ht=(e,t)=>(0,an.ConfigurationSchema)(e,{indexType:{model:Hs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),yd=(0,an.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ht("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:ht("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wd=(0,an.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ht("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:ht("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}},walksIndex:ht("RgfaWalksIndex",""),walkChunk:{type:"integer",defaultValue:65536},walkStepBudget:{type:"integer",defaultValue:4e6},walkByteBudget:{type:"integer",defaultValue:8e6},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:yd},{explicitlyTyped:!0,preProcessSnapshot:kr}),$s=wd;function Rr(e){e.addAdapterType(()=>new Os.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:kr,configSchema:$s,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-KOIMYOR3.js").then(t=>t.default)}))}var kd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Rd(e){return Er(e).toLowerCase().endsWith(".gbz.db")}function Sd(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 xd(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Rd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Dr(e))return Vr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Sr(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Sd),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>xd(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>kd.has(n)?"GraphTrack":t(n,r))}var zs=m(ne(),1),sn=m(ic(),1),xr=m(ac(),1),Xs=m(sc(),1);function _s(e){let t;if(q(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Ld(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Ws(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Md(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>q(n)&&Array.isArray(n.displays)?n.displays.filter(r=>q(r)&&r.type==="LinearGraphDisplay"):[])}function js(e,t,n){let r=[],o=ut(e),a=new Set(o.map(i=>q(i)?i.id:void 0));for(let i of o){if(q(i)&&i.id===t)for(let s of Md(i)){let c=_s(s.hoverHighlight);c&&Ws(c,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(q(i)&&i.type==="GraphGenomeView"&&Ld(i,t,a)){let s=_s(i.hoverHighlight);s&&Ws(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ee=m(ue(),1),vd=(0,Xs.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,sn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,sn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,sn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Td=(0,xr.observer)(function({model:t,region:n}){let{classes:r}=vd(),o=t.getHighlightCoords(n);return o?(0,Ee.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Gd=(0,xr.observer)(function({model:t}){let{views:n}=(0,zs.getSession)(t);return(0,Ee.jsx)(Ee.Fragment,{children:js([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Ee.jsx)(Td,{model:t,region:o},`graph-hover-${r}`))})}),Ys=Gd;var Us=m(ue(),1),Nd="LinearGenomeView-TracksContainerComponent";function Lr(e){e.contributeToExtensionPoint(Nd,({model:t})=>(0,Us.jsx)(Ys,{model:t},"graphgenomeview-hover-highlight"))}var Ks=m(me(),1);function Ad(e){return e.views(t=>({get adapterConfig(){return le(t,t.parentTrack.configuration)}}))}function Mr(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Ks.DisplayType&&mr.includes(t.name)&&t.extendStateModel(Ad),t))}var qs="GraphGenomeView";var Js="6.9.2";var vr=class extends Zs.default{constructor(){super(...arguments);this.name=qs;this.version=Js}install(n){ur(n),fr(n),lr(n),gr(n),Lr(n),Rr(n),wr(n),Dn(n),Vn(n),Sr(n),Mr(n),n.addRpcMethod(()=>new nt(n)),n.addRpcMethod(()=>new tt(n)),n.addRpcMethod(()=>new et(n)),n.addRpcMethod(()=>new Qe(n))}configure(n){try{(0,Qs.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:_t,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{vr as default};
 //# sourceMappingURL=jbrowse-plugin-graphgenomeviewer.esm.js.map