jbrowse-plugin-graphgenomeviewer 7.4.1 → 7.4.2

package/dist/chunks/{chunk-4XM5OBD5.js → chunk-ZG2CQXOW.js}

@@ -1,2 +1,2 @@
-import{e as g}from"./chunk-MVVXRZXV.js";import{e as C}from"./chunk-IKJZPPOA.js";function A(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function ne(e){let t=g(e,"assemblyNames"),n=A(t)?t.slice(1):[];return n.length>0?n:void 0}function M(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||C(e.walksLocation))}function te(e){return e.type==="GbzBaseSyntenyAdapter"||M(e)}function re(e){let{defaultHaplotypes:t}=e;return M(e)&&A(t)&&t.length>0?t:void 0}function se(e){let t=g(e,"assemblyNames");return A(t)?t[0]:void 0}function oe(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,t){return typeof e.get=="function"?e.get(t):e[t]}function y(e,t){return e.find(n=>n.trackId===t)}function h(e){return`${e.trackId} ${e.name??""}`}var $=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),R=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function ve(e,t){let n=t?y(e,t):void 0;return n||e.filter(s=>$.has(s.adapterType)).find(s=>R.test(h(s)))}var O=/^\w+=[^;]*(;\w+=[^;]*)*$/;function G(e){let t=i(e,"name");if(!(typeof t!="string"||!O.test(t)))return Object.fromEntries(t.split(";").map(n=>{let r=n.indexOf("=");return[n.slice(0,r),n.slice(r+1)]}))}function d(e,t){let n=i(e,t);return n!==void 0?n:i(e,"INFO")?.[t]??G(e)?.[t]}var P=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],U=["RUL","period","PERIOD","consensusSize","unit","unitLength"],H=["TRID","REPID","VARID","ID","name","id"];function T(e,t){for(let n of t){let r=d(e,n),s=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(s!==""&&s!==".")return s}}var D=/^[ACGTURYSWKMBDHVN]+$/i;function v(e){let t=Number(T(e,U));if(Number.isFinite(t)&&t>0)return Math.round(t);let n=T(e,P);return n&&D.test(n)?n.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=n===""||n===null||n===void 0?NaN:Number(n);return Number.isFinite(r)?r:void 0})}function N(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=String(n??"").trim();return r===""||r==="."?void 0:r})}var w="<CNV:TR>";function j(e){let t=N(i(e,"ALT"));if(!t.includes(w))return;let n=m(d(e,"RN")),r=N(d(e,"RUS")),s=m(d(e,"RUL")),o=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return t.map((u,f)=>{let p=n[f]??(u===w?1:0),b=0,S=0;for(let F=0;F<p;F++,c++){let x=r[c],L=s[c]??(x&&D.test(x)?x.length:void 0),_=o[c],I=a[c]??(L&&_!==void 0?Math.round(L*_):void 0);I!==void 0&&(b+=I,S++)}return u===w&&p>0&&S===p?b:void 0})}function V(e,t,n){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((s,o)=>{let a=s===""?NaN:Number(s),c=a>0?t[a-1]:n;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:o+1}:{}}]})}function W(e,t,n){let r=i(e,"samples"),s={};for(let[o,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,b)=>p!==void 0&&p>0?[c[b]===void 0?{bp:p}:{bp:p,spanningReads:c[b]}]:[]),f=u.length>0||!t?u:V(N(a.GT)[0],t,n);f.length>0&&(s[o]=f)}return Object.keys(s).length>0?s:void 0}function Y(e,t){let n=d(e,"start"),r=d(e,"end"),s=m(d(e,"SVLEN"))[0];return t&&s!==void 0?{start:n+1,end:n+1+s}:{start:n,end:r}}function je(e){let t=[];for(let n of e){let r=j(n),{start:s,end:o}=Y(n,r!==void 0),a=v(n);if(!(o>s)||a===void 0)continue;let c=d(n,"refName"),u=T(n,P),f=T(n,H);t.push({key:`${c}:${s}-${o}`,name:(f&&!O.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(s+1).toLocaleString("en-US")}-${o.toLocaleString("en-US")}`),refName:c,start:s,end:o,unit:a,motif:u,calls:W(n,r,o-s)})}return t.sort((n,r)=>n.start-r.start)}function k(e){let t=[];for(let n of[...e].sort((r,s)=>r.start-s.start)){let r=t.at(-1);r&&n.start<=r.end?r.end=Math.max(r.end,n.end):t.push({...n})}return t}function E(e){let t=[],n=new Map;for(let r of[...e].sort((s,o)=>s.start-o.start)){let s=`${r.refName}	${r.strand}	${r.name}`,o=n.get(s);if(o&&r.start<o.end)o.end=Math.max(o.end,r.end),o.exons=k([...o.exons,...r.exons]);else{let a={...r,exons:k(r.exons)};t.push(a),n.set(s,a)}}return t}var K=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),J=/gene|refseq|gencode|ensembl|annotation/i,q=new Set(["BedTabixAdapter","BedAdapter"]);function nn(e,t){let n=t?y(e,t):void 0;if(n)return n;let r=e.filter(s=>K.has(s.adapterType)&&!R.test(h(s)));return r.find(s=>J.test(h(s)))??r.find(s=>!q.has(s.adapterType))}function tn(e,t){let n=e.tracks?.find(r=>g(r.configuration,"trackId")===t)?.displays[0];return n?g(n.configuration,"filter")??[]:[]}var z=new Set(["chromosome","region","contig","supercontig","scaffold"]),X=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function B(e,t){let n=i(e,"type");typeof n=="string"&&X.has(n)&&t.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let s of r??[])B(s,t)}function rn(e){let t=[];for(let n of e){let r=i(n,"gene_name")??i(n,"name")??i(n,"gene")??i(n,"gene_id"),s=i(n,"start"),o=i(n,"end");if(!r||!(o>s)||z.has(i(n,"type")))continue;let a=[];B(n,a),t.push({name:r,refName:i(n,"refName"),start:s,end:o,strand:i(n,"strand")??0,exons:a.length?k(a):[{start:s,end:o}]})}return E(t)}var l=JBrowseExports["tss-react/mui"],Q=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var on=Q("makeStyles"),an=l&&l.__esModule?l.default:l;export{ne as a,M as b,te as c,re as d,se as e,oe as f,$ as g,ve as h,je as i,K as j,nn as k,tn as l,rn as m,on as n};
-//# sourceMappingURL=chunk-4XM5OBD5.js.map
+import{e as g}from"./chunk-MVVXRZXV.js";import{e as C}from"./chunk-IKJZPPOA.js";function A(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function ne(e){let t=g(e,"assemblyNames"),n=A(t)?t.slice(1):[];return n.length>0?n:void 0}function M(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||C(e.walksLocation))}function te(e){return e.type==="GbzBaseSyntenyAdapter"||M(e)}function re(e){let{defaultHaplotypes:t}=e;return M(e)&&A(t)&&t.length>0?t:void 0}function se(e){let t=g(e,"assemblyNames");return A(t)?t[0]:void 0}function oe(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,t){return typeof e.get=="function"?e.get(t):e[t]}function y(e,t){return e.find(n=>n.trackId===t)}function h(e){return`${e.trackId} ${e.name??""}`}var $=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),R=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function je(e,t){let n=t?y(e,t):void 0;return n||e.filter(s=>$.has(s.adapterType)).find(s=>R.test(h(s)))}var O=/^\w+=[^;]*(;\w+=[^;]*)*$/;function G(e){let t=i(e,"name");if(!(typeof t!="string"||!O.test(t)))return Object.fromEntries(t.split(";").map(n=>{let r=n.indexOf("=");return[n.slice(0,r),n.slice(r+1)]}))}function d(e,t){let n=i(e,t);return n!==void 0?n:i(e,"INFO")?.[t]??G(e)?.[t]}var P=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],U=["RUL","period","PERIOD","consensusSize","unit","unitLength"],H=["TRID","REPID","VARID","ID","name","id"];function T(e,t){for(let n of t){let r=d(e,n),s=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(s!==""&&s!==".")return s}}var D=/^[ACGTURYSWKMBDHVN]+$/i;function v(e){let t=Number(T(e,U));if(Number.isFinite(t)&&t>0)return Math.round(t);let n=T(e,P);return n&&D.test(n)?n.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=n===""||n===null||n===void 0?NaN:Number(n);return Number.isFinite(r)?r:void 0})}function N(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=String(n??"").trim();return r===""||r==="."?void 0:r})}var w="<CNV:TR>";function j(e){let t=N(i(e,"ALT"));if(!t.includes(w))return;let n=m(d(e,"RN")),r=N(d(e,"RUS")),s=m(d(e,"RUL")),o=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return t.map((u,f)=>{let p=n[f]??(u===w?1:0),b=0,S=0;for(let F=0;F<p;F++,c++){let x=r[c],L=s[c]??(x&&D.test(x)?x.length:void 0),_=o[c],I=a[c]??(L&&_!==void 0?Math.round(L*_):void 0);I!==void 0&&(b+=I,S++)}return u===w&&p>0&&S===p?b:void 0})}function V(e,t,n){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((s,o)=>{let a=s===""?NaN:Number(s),c=a>0?t[a-1]:n;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:o+1}:{}}]})}function W(e,t,n){let r=i(e,"samples"),s={};for(let[o,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,b)=>p!==void 0&&p>0?[c[b]===void 0?{bp:p}:{bp:p,spanningReads:c[b]}]:[]),f=u.length>0||!t?u:V(N(a.GT)[0],t,n);f.length>0&&(s[o]=f)}return Object.keys(s).length>0?s:void 0}function Y(e,t){let n=d(e,"start"),r=d(e,"end"),s=m(d(e,"SVLEN"))[0];return t&&s!==void 0?{start:n+1,end:n+1+s}:{start:n,end:r}}function Ve(e){let t=[];for(let n of e){let r=j(n),{start:s,end:o}=Y(n,r!==void 0),a=v(n);if(!(o>s)||a===void 0)continue;let c=d(n,"refName"),u=T(n,P),f=T(n,H);t.push({key:`${c}:${s}-${o}`,name:(f&&!O.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(s+1).toLocaleString("en-US")}-${o.toLocaleString("en-US")}`),refName:c,start:s,end:o,unit:a,motif:u,calls:W(n,r,o-s)})}return t.sort((n,r)=>n.start-r.start)}function k(e){let t=[];for(let n of[...e].sort((r,s)=>r.start-s.start)){let r=t.at(-1);r&&n.start<=r.end?r.end=Math.max(r.end,n.end):t.push({...n})}return t}function E(e){let t=[],n=new Map;for(let r of[...e].sort((s,o)=>s.start-o.start)){let s=`${r.refName}	${r.strand}	${r.name}`,o=n.get(s);if(o&&r.start<o.end)o.end=Math.max(o.end,r.end),o.exons=k([...o.exons,...r.exons]);else{let a={...r,exons:k(r.exons)};t.push(a),n.set(s,a)}}return t}var K=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),J=/gene|refseq|gencode|ensembl|annotation/i,q=new Set(["BedTabixAdapter","BedAdapter"]);function tn(e,t){let n=t?y(e,t):void 0;if(n)return n;let r=e.filter(s=>K.has(s.adapterType)&&!R.test(h(s)));return r.find(s=>J.test(h(s)))??r.find(s=>!q.has(s.adapterType))}function rn(e,t){let n=e.tracks?.find(r=>g(r.configuration,"trackId")===t)?.displays[0];return n?g(n.configuration,"filter")??[]:[]}var z=new Set(["chromosome","region","contig","supercontig","scaffold"]),X=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function B(e,t){let n=i(e,"type");typeof n=="string"&&X.has(n)&&t.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let s of r??[])B(s,t)}function sn(e){let t=[];for(let n of e){let r=i(n,"gene_name")??i(n,"name")??i(n,"gene")??i(n,"gene_id"),s=i(n,"start"),o=i(n,"end");if(!r||!(o>s)||z.has(i(n,"type")))continue;let a=[];B(n,a),t.push({name:r,refName:i(n,"refName"),start:s,end:o,strand:i(n,"strand")??0,exons:a.length?k(a):[{start:s,end:o}]})}return E(t)}var l=JBrowseExports["tss-react/mui"],Q=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var an=Q("makeStyles"),cn=l&&l.__esModule?l.default:l;export{ne as a,M as b,te as c,re as d,se as e,oe as f,$ as g,je as h,Ve as i,K as j,tn as k,rn as l,sn as m,an as n};
+//# sourceMappingURL=chunk-ZG2CQXOW.js.map

package/dist/chunks/{chunk-4XM5OBD5.js.map → chunk-ZG2CQXOW.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
   "sourcesContent": ["import { readConfObject } from '@jbrowse/core/configuration'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  const lanes = isStringArray(assemblyNames) ? assemblyNames.slice(1) : []\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  return isStringArray(assemblyNames) ? assemblyNames[0] : undefined\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
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package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

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highlighted...",onClick:()=>{R(e).queueDialog(a=>[ur,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...q(tr.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Tt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=F(e.chosenLayoutMode),r=Zn.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${_t(o)}${o.value==="force"?` (${r})`:""}`,icon:Rn,subMenu:[..._o.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?Zn.map(([i,p])=>({...a,label:`${_t(n)} (${p})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:_t(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:Tn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:q(Tt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:or,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of nn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))nt(t,n);return t}}));var at=Qn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ae(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Xo(o),n=R(e);return r===void 0?void 0:Ko(Pe(n,r),Pe(n,t.assemblyName))},cutChangedFrom(t){let o=$o(F(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function zt(){return M.compose("GraphGenomeView",Sn,at,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:kt(ze),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:kt(Te)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(ue(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${ce(a)}) \u2014 zoom in to view graph (max ${ce(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ue(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=R(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Rt(n,r)):void 0):o(r&&Rt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),H(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(ue(t)))},afterAttach(){e.graph||e.load(),L(e,C(()=>e.walkStrip,()=>{e.loadedTrackId&&!F(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ii=kn()({});function $t(e){e.addViewType(()=>new Mn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:zt(),launchKeys:ii,ReactComponent:ee(()=>import("./chunks/GraphGenomeView-52OPGZER.js"))}))}var Jt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function si(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Jt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Yt(e){e.addTrackType(()=>{let t=O("GraphTrack",{},{baseConfiguration:yn(e),explicitIdentifier:"trackId"}),o=new hn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:bn(e,"GraphTrack",t)});for(let r of si(e))o.addDisplayType(r);return o})}function Ut(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var it=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var ea=it&&it.__esModule?it.default:it;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],pi=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),ta=pi("trackHeightConfigSchemaFields"),em=be&&be.__esModule?be.default:be;function oa(){return O("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",ze),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Te),defaultValue:"nodes"},...ta({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],ci=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ra=ci("computeSvgReady");var pm=fe&&fe.__esModule?fe.default:fe;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var na=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ui=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),aa=ui("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var Me=JBrowseExports["@jbrowse/render-core/displayPhase"],ia=e=>Me!=null&&e in Object(Me)?Me[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),sa=ia("computeActivityPhase");var pa=ia("computeDisplayStatusPhase"),lm=Me&&Me.__esModule?Me.default:Me;function Xt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var di=new Set(["scale","translateX","translateY"]);function mi(e){return Object.fromEntries(Object.keys(br.properties).filter(t=>!di.has(t)).map(t=>[t,e[t]]))}var Kt=10;function li(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/Kt:void 0}var gi=ee(()=>import("./chunks/GraphTrackSettingsDialog-JHIP2F5N.js"));function ca(e){return M.compose("LinearGraphDisplay",mn,na(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:zo(jo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&St(r))},get coarseAboveBpPerPx(){return li(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=Kt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${ce(o.end-o.start)}, max ${ce(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ra({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return pa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>sa({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(Kt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Ur(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Xt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Xr(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await R(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&Yo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),L(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;L(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Xt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...mi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&R(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Uo(o))return[];let n=Ae(o),a=St(r),i=t.haplotypeNames,p=t.subgraphHaplotypes,s=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:p?p.length===0:!n&&!a,onClick:()=>{s([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:p===void 0,onClick:()=>{s(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(p?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){R(t).queueDialog(o=>[gi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-IXWB7R54.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:sn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:pn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...aa(t)]}}))}function qt(e){e.addDisplayType(()=>{let t=oa();return Object.assign(new ea({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ca(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-EF2GE7X7.js"))}),{adapterCapabilities:["getSubgraph"]})})}function hi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Le(t,o,r)}:e}var yi=O("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:z("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:hi}),ua=yi;function Zt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:ua,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-XC75BCG3.js").then(t=>t.default)}))}function da(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Le(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Le(`${t}.links.bed.gz`,o,r)}:e}function bi(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(da(typeof t=="object"&&t!==null?{...e,coarse:da({baseUri:o,csi:r,...t})}:e))}var fi=O("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:z("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:z("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wi=O("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:z("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:z("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:z("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fi},{explicitlyTyped:!0,preProcessSnapshot:bi}),ma=wi;function Qt(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ma,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-56X2U424.js").then(t=>t.default)}))}var Mi=O("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:z("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),la=Mi;function eo(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:la,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-ECW557IS.js").then(t=>t.default)}))}var ki=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Si(e){return gt(e).toLowerCase().endsWith(".gbz.db")}function xi(e){let t=e.adapter;return t?.type!==void 0&&Kr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ri(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ti(e,t,o){let r=n=>Fo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Si(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Ho(e))return r("RgfaTabixAdapter");if(gt(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function to(e){e.addToExtensionPoint("Core-preProcessTrackConfig",xi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ri),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ti(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>ki.has(o)?"GraphTrack":t(o,r))}function ga(e){let t;if($(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Gi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ha(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Li(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>$(o)&&Array.isArray(o.displays)?o.displays.filter(r=>$(r)&&r.type==="LinearGraphDisplay"):[])}function ya(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>$(i)?i.id:void 0));for(let i of n){if($(i)&&i.id===t)for(let p of Li(i)){let s=ga(p.hoverHighlight);s&&ha(s,o)&&r.push({key:typeof p.id=="string"?p.id:"graph-track",region:s})}if($(i)&&i.type==="GraphGenomeView"&&Gi(i,t,a)){let p=ga(i.hoverHighlight);p&&ha(p,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:p})}}return r}var vi=an()(e=>({highlight:{height:"100%",position:"absolute",background:De(e.palette.primary.main,.08),borderLeft:`1px solid ${De(e.palette.primary.main,.4)}`,borderRight:`1px solid ${De(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ai=ft(function({model:t,region:o}){let{classes:r}=vi(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Pi=ft(function({model:t}){let{views:o}=R(t);return A(fo,{children:ya([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ai,{model:t,region:n},`graph-hover-${r}`))})}),ba=Pi;var Ci="LinearGenomeView-TracksContainerComponent";function oo(e){e.contributeToExtensionPoint(Ci,({model:t})=>A(ba,{model:t},"graphgenomeview-hover-highlight"))}function Bi(e){return e.views(t=>({get adapterConfig(){return qr(t,t.parentTrack.configuration)}}))}function ro(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof ln&&Jt.includes(t.name)&&t.extendStateModel(Bi),t))}var fa="GraphGenomeView";var wa="7.4.1";var no=class extends cn{constructor(){super(...arguments);this.name=fa;this.version=wa}install(o){$t(o),qt(o),Yt(o),Ut(o),oo(o),Qt(o),Zt(o),Et(o),eo(o),Vt(o),to(o),ro(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{ho(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{no as default};
+`);return[{type:"radio",label:"Every sample",checked:o===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:o!==void 0&&!r(t),onClick:()=>{x(e).queueDialog(n=>[sr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return q([{value:void 0,label:"None"},...e.walkRowGroupFields.map(o=>({value:o,label:o}))],t,o=>{e.setWalkRowGroupBy(o===void 0?void 0:{field:o})})},tubeMapPanelMenuItems(){let{graph:t,walkRowSampleTable:o}=e,{field:r}=e.facetSetting,n=r===""?e.walkRowGroupBy?.field:void 0,a=i=>!!t&&Ue(t,i).length>1;return[...q(jr.map(i=>({value:i.field,label:i.label,disabled:i.field!==""&&!a({by:i.field})})),n?void 0:r,i=>{e.setFacet(i),i===""&&e.setWalkRowGroupBy(void 0)}),...q(e.walkRowGroupFields.map(i=>({value:i,label:`By ${i}`,disabled:!o||!a({by:"column",field:i,table:o})})),n,i=>{e.setFacet(""),e.setWalkRowGroupBy({field:i})})]},layoutOptionMenuItems({repeat:t=!0}={}){return[...se.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:q(dr.map(({bp:o,label:r})=>({value:o,label:r,disabled:o>0&&e.graph?.reads!==void 0})),e.graph?.reads?0:e.tubeMapFold,e.setTubeMapFold)},{label:"Panels",subMenu:this.tubeMapPanelMenuItems()},{label:"Routes",subMenu:q(gr,e.tubeMapRoutes,e.setTubeMapRoutes)},...e.walkRowGroupFields.length>0?[{label:"Tube color",subMenu:q(["",...e.walkRowGroupFields].map(o=>({value:o,label:o?`By ${o}`:"By role"})),e.tubeMapColorBy,e.setTubeMapColorBy)}]:[]]:[],...t&&e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:q(e.repeatOptions,e.selectedRepeat?.key??"",e.setRepeatKey)}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:q(Re.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:Tn,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&Un(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}},{label:"Copy figure spec",icon:Sn,disabled:e.figureSpecUnavailable!==void 0,disabledHelpText:e.figureSpecUnavailable,onClick:()=>{let t=e.figureSpec(),o=x(e);navigator.clipboard.writeText(`${JSON.stringify(t,null,2)}
+`).then(()=>{o.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(r=>{o.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>ur;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{x(e).queueDialog(a=>[pr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{x(e).queueDialog(a=>[cr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...q(er.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Gt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=F(e.chosenLayoutMode),r=Xn.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${zt(o)}${o.value==="force"?` (${r})`:""}`,icon:xn,subMenu:[...Do.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?Xn.map(([i,s])=>({...a,label:`${zt(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:zt(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:Rn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:q(Gt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:tr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of rn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))nt(t,n);return t}}));var at=Kn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ae(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Uo(o),n=x(e);return r===void 0?void 0:Xo(Pe(n,r),Pe(n,t.assemblyName))},cutChangedFrom(t){let o=zo(F(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function $t(){return M.compose("GraphGenomeView",kn,at,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:St(ze),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:St(Re)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(ce(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${pe(a)}) \u2014 zoom in to view graph (max ${pe(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ce(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=x(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Tt(n,r)):void 0):o(r&&Tt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),H(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(ce(t)))},afterAttach(){e.graph||e.load(),G(e,C(()=>e.walkStrip,()=>{e.loadedTrackId&&!F(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var oi=Mn()({});function Jt(e){e.addViewType(()=>new fn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:$t(),launchKeys:oi,ReactComponent:ee(()=>import("./chunks/GraphGenomeView-UCOAMRF7.js"))}))}var Yt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function ri(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Yt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Ut(e){e.addTrackType(()=>{let t=j("GraphTrack",{},{baseConfiguration:hn(e),explicitIdentifier:"trackId"}),o=new gn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:yn(e,"GraphTrack",t)});for(let r of ri(e))o.addDisplayType(r);return o})}function Xt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var it=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var qn=it&&it.__esModule?it.default:it;var ye=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],ni=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Zn=ni("trackHeightConfigSchemaFields"),em=ye&&ye.__esModule?ye.default:ye;function Qn(){return j("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",ze),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Re),defaultValue:"nodes"},...Zn({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var be=JBrowseExports["@jbrowse/core/svg/svgReady"],ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ea=ai("computeSvgReady");var pm=be&&be.__esModule?be.default:be;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ta=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ii=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),oa=ii("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var fe=JBrowseExports["@jbrowse/render-core/displayPhase"],ra=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),na=ra("computeActivityPhase");var aa=ra("computeDisplayStatusPhase"),lm=fe&&fe.__esModule?fe.default:fe;function Kt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var si=new Set(["scale","translateX","translateY"]);function pi(e){return Object.fromEntries(Object.keys(yr.properties).filter(t=>!si.has(t)).map(t=>[t,e[t]]))}var qt=10;function ci(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/qt:void 0}var ui=ee(()=>import("./chunks/GraphTrackSettingsDialog-MR7X75EY.js"));function ia(e){return M.compose("LinearGraphDisplay",dn,ta(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:_o(Fo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&xt(r))},get coarseAboveBpPerPx(){return ci(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=qt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${pe(o.end-o.start)}, max ${pe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ea({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return aa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>na({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(qt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Yr(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Kt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Ur(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;G(t,()=>{o?.abort()}),G(t,C(()=>{let n=t.sourceAdapter;return n&&Jo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),G(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),G(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;G(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),G(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),G(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Kt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...pi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Yo(o))return[];let n=Ae(o),a=xt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=u=>{t.setSubgraphHaplotypes(u),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[ui,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-Z7YIXVQ5.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:an,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:sn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...oa(t)]}}))}function Zt(e){e.addDisplayType(()=>{let t=Qn();return Object.assign(new qn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ia(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-AJ5OZN27.js"))}),{adapterCapabilities:["getSubgraph"]})})}function di(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Ge(t,o,r)}:e}var mi=j("MinigraphBubbleAdapter",{bubblesLocation:N("/path/to/graph.bb.bed.gz"),index:_("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:di}),sa=mi;function Qt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:sa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-PEQK5NII.js").then(t=>t.default)}))}function pa(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Ge(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Ge(`${t}.links.bed.gz`,o,r)}:e}function li(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(pa(typeof t=="object"&&t!==null?{...e,coarse:pa({baseUri:o,csi:r,...t})}:e))}var gi=j("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:N("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),hi=j("RgfaTabixAdapter",{segmentsLocation:N("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:N(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:gi},{explicitlyTyped:!0,preProcessSnapshot:li}),ca=hi;function eo(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-Q63YLPK4.js").then(t=>t.default)}))}var yi=j("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:N("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:N(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),ua=yi;function to(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-N5PFI4LS.js").then(t=>t.default)}))}var bi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function wi(e){return lt(e).toLowerCase().endsWith(".gbz.db")}function fi(e){let t=e.adapter;return t?.type!==void 0&&Xr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Mi(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function ki(e,t,o){let r=n=>Ho({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&wi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Vo(e))return r("RgfaTabixAdapter");if(lt(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function oo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",fi),e.addToExtensionPoint("Core-preProcessTrackConfig",Mi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>ki(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>bi.has(o)?"GraphTrack":t(o,r))}function da(e){let t;if(z(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Si(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function xi(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>z(o)&&Array.isArray(o.displays)?o.displays.filter(r=>z(r)&&r.type==="LinearGraphDisplay"):[])}function la(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>z(i)?i.id:void 0));for(let i of n){if(z(i)&&i.id===t)for(let s of xi(i)){let p=da(s.hoverHighlight);p&&ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if(z(i)&&i.type==="GraphGenomeView"&&Si(i,t,a)){let s=da(i.hoverHighlight);s&&ma(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ri=nn()(e=>({highlight:{height:"100%",position:"absolute",background:De(e.palette.primary.main,.08),borderLeft:`1px solid ${De(e.palette.primary.main,.4)}`,borderRight:`1px solid ${De(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ti=bt(function({model:t,region:o}){let{classes:r}=Ri(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Gi=bt(function({model:t}){let{views:o}=x(t);return A(fo,{children:la([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ti,{model:t,region:n},`graph-hover-${r}`))})}),ga=Gi;var Li="LinearGenomeView-TracksContainerComponent";function ro(e){e.contributeToExtensionPoint(Li,({model:t})=>A(ga,{model:t},"graphgenomeview-hover-highlight"))}function vi(e){return e.views(t=>({get adapterConfig(){return Kr(t,t.parentTrack.configuration)}}))}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof mn&&Yt.includes(t.name)&&t.extendStateModel(vi),t))}var ha="GraphGenomeView";var ya="7.4.2";var ao=class extends pn{constructor(){super(...arguments);this.name=ha;this.version=ya}install(o){Jt(o),Zt(o),Ut(o),Xt(o),ro(o),eo(o),Qt(o),Et(o),to(o),Ht(o),oo(o),no(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{yo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{ao as default};
 //# sourceMappingURL=jbrowse-plugin-graphgenomeviewer.esm.js.map