jbrowse-plugin-graphgenomeviewer 7.1.6 → 7.1.8

package/dist/chunks/{ChooseWalksDialog-UXLFZTZJ.js → ChooseWalksDialog-SM326TOX.js}

@@ -1,2 +1,2 @@
-import{a as t}from"./chunk-IBWORBGY.js";import"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as l,d as i}from"./chunk-JMBDTNUR.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftWalks(e)},onClose:s})}),k=h;export{k as default};
-//# sourceMappingURL=ChooseWalksDialog-UXLFZTZJ.js.map
+import{a as t}from"./chunk-IBWORBGY.js";import"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as l,d as i}from"./chunk-JMBDTNUR.js";var h=i(function({model:o,onClose:s}){let{walkChoices:a}=o;return l(t,{title:"Choose haplotypes",label:"Haplotypes",testId:"graph-choose-walks",caption:`${a.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`,options:a.map(e=>e.name),initial:o.walkLayers.map(e=>e.walk),optionLabel:e=>o.walkLabel(e),confirmLabel:e=>e.length>0?"Highlight these":"Clear highlights",onPick:e=>{o.liftAmongChoices(e)},onClose:s})}),k=h;export{k as default};
+//# sourceMappingURL=ChooseWalksDialog-SM326TOX.js.map

package/dist/chunks/ChooseWalksDialog-SM326TOX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/ChooseWalksDialog.tsx"],
+  "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport PickNamesDialog from './PickNamesDialog'\n\nimport type { GraphPaneModel } from '../model'\n\ntype WalkPicker = Pick<\n  GraphPaneModel,\n  'walkChoices' | 'walkLayers' | 'walkLabel' | 'liftAmongChoices'\n>\n\n// Which haplotypes to highlight, for a graph with more walks than a menu can\n// list\nconst ChooseWalksDialog = observer(function ChooseWalksDialog({\n  model,\n  onClose,\n}: {\n  model: WalkPicker\n  onClose: () => void\n}) {\n  const { walkChoices } = model\n  return (\n    <PickNamesDialog\n      title=\"Choose haplotypes\"\n      label=\"Haplotypes\"\n      testId=\"graph-choose-walks\"\n      caption={`${walkChoices.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`}\n      options={walkChoices.map(c => c.name)}\n      initial={model.walkLayers.map(l => l.walk)}\n      optionLabel={name => model.walkLabel(name)}\n      confirmLabel={picked =>\n        picked.length > 0 ? 'Highlight these' : 'Clear highlights'\n      }\n      onPick={picked => {\n        model.liftAmongChoices(picked)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseWalksDialog\n"],
+  "mappings": "+IAaA,IAAMA,EAAoBC,EAAS,SAA2B,CAC5D,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,GAAM,CAAE,YAAAC,CAAY,EAAIF,EACxB,OACEG,EAACC,EAAA,CACC,MAAM,oBACN,MAAM,aACN,OAAO,qBACP,QAAS,GAAGF,EAAY,OAAO,eAAe,CAAC,8FAC/C,QAASA,EAAY,IAAIG,GAAKA,EAAE,IAAI,EACpC,QAASL,EAAM,WAAW,IAAIM,GAAKA,EAAE,IAAI,EACzC,YAAaC,GAAQP,EAAM,UAAUO,CAAI,EACzC,aAAcC,GACZA,EAAO,OAAS,EAAI,kBAAoB,mBAE1C,OAAQA,GAAU,CAChBR,EAAM,iBAAiBQ,CAAM,CAC/B,EACA,QAASP,EACX,CAEJ,CAAC,EAEMQ,EAAQX",
+  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
+}

package/dist/chunks/{GbzBaseSyntenyAdapter-WEQKJ5ZF.js → GbzBaseSyntenyAdapter-3HGD7PKF.js}

@@ -1,2 +1,2 @@
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Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function we(n,s){return`${u(n)}#${n.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:n,assemblyName:s,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:i}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,d=we(c,n),g={uniqueId:d,assemblyName:s,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:i,syntenyId:d,mate:{refName:c.contig,start:p,end:l,assemblyName:e}};return new ae(g)}}function Se({pair:n,lane:s,mateLane:t}){return ie({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:s,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:t,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Pe=12e4;function Ne(n,s){let t=new Map;for(let a of n)for(let{name:r,start:o,end:i}of a.walkSpans()){let c=u(r);if(s.has(c)){let p=`${c}#${r.contig}`,l=t.get(p);l?l.push([o,i]):t.set(p,[[o,i]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Pe&&(e=Math.max(e,o))}}return e}function _(n,s){return n instanceof U&&(n.message=`Zoom in to about ${j(n.fitsBp)} to see ${s}`),n}var le=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),D=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await ce(t,this.pluginManager),r=a.location,o=await Z.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await $(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,i),referenceSamples:c});return{db:o,anchor:i,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?ee(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let i=u(o.name),c=r.get(i);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(i,{prefix:i,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a}=await this.graph(t),r=C(this),o=[];for(let i of await this.getHaplotypes(t))i.sample!==a&&o.push({name:q(r,i.prefix),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,lanes:o}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,i=o===a?void 0:P(this,o),c=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),i)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>M(r,a)&&(e===void 0||F(u(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:i,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:d,end:g}=le(t);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${i} has no indexed path ${l} in this graph`);let w=this.keepPredicate(e.haplotypes);if(w!==void 0&&!r.hasHaplotypeIndex)throw new B(c);let f=await X(r,y,d,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:w}).catch(x=>{throw _(x,"the graph")});return typeof f=="string"?f:ne(f,{start:d,end:g},e.walkRows)}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=P(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:i,end:c}=t,p=P(this,e.targetAssemblyName),l=C(this),d=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await I(`Reading graph ${o}:${i.toLocaleString()}-${c.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:i,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:d}).catch(f=>{throw _(z(f,y,c-i)??f,"lanes")})):[]).flatMap(f=>{let x=f.resolved?xe({alignment:f,assemblyName:r,refName:o,lane:q(l,u(f.name))}):void 0;return x===void 0?[]:[x]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:i,end:c}=t,l=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),d=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),w=this.getConf("context"),f=(m,h)=>r.getSubgraphs({path:m,start:i,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>d.has(u(S))}),x=async m=>{let h=await f(m,w).catch(b=>{throw _(z(b,y,c-i)??b,"lanes")}),S=Ne(h,d),R=Math.ceil(S/2)+2e3;return S>0&&R>w?f(m,R).catch(b=>{if(b instanceof W)return h;throw b}):h};return(g&&l.length>0?await I(se(e),a.statusCallback,()=>x(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(b=>R.flatMap(me=>m.pairAlignments({target:b,query:me,bases:!1}).map(fe=>Se({pair:fe,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=le(t);return te(async r=>{let{db:o,anchor:i,unreadableIndex:c}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new B(c);if(a.assemblyName===i){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let d of l)r.next(d)}r.complete()},e.signal)}};export{B as NoHaplotypeIndexError,de as PairTargetError,D as default,Ne as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-WEQKJ5ZF.js.map
+import{a as ae,b as re,c as de,d as oe,e as se,f as q,g as ie}from"./chunk-IP3ORVTU.js";import{a as te}from"./chunk-KOB7YIMR.js";import{a as W,b as Z,c as U,d as u,e as M,f as $,g as k,h as E,i as z,k as X}from"./chunk-IT7HZNZO.js";import"./chunk-TFPHVH5H.js";import{b as O,c as H}from"./chunk-TVFR5KBQ.js";import"./chunk-Y7UUDKJL.js";import"./chunk-T4HOC6O3.js";import{a as ne}from"./chunk-HVBY3TGB.js";import{a as V,c as L,m as ee}from"./chunk-SQUFY3QO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as F,f as P,g as C}from"./chunk-KM3QNC77.js";import"./chunk-E7J6SB5P.js";import{b as G,e as Y,f as J,g as K}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as j,o as I}from"./chunk-TENPGIPX.js";function A(n){let s=/\.gbz\.db$/i;return s.test(n)?n.replace(s,".haplotype-index.db"):void 0}function he(n){return J(n)&&A(Y(n))?K(n,s=>A(s)):void 0}function ue(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,s){let t=he(n);if(!t)return{};try{return await N(t,s).stat(),{location:t}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(n,s){if(n.length<=s)return n;let t=n.length/s;return Array.from({length:s},(e,a)=>n[Math.floor(a*t)])}var pe=(n,s)=>n.path.some(t=>s.has(t.name)),v=class{constructor(s,t){this.file=s;this.tabix=t;this.whole=L({setup:async({signal:s})=>{let{size:t}=await this.file.stat();if(t>ye)throw new T(t);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await V(e):e);return H(a)}})}async readIndexed(s,t,e){let a=1/0,r=-1/0;for(let i of t){let c=Number(i);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:i=>{let c=O(i);c&&pe(c,t)&&o.push(c)}}),o}async readsOver(s,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,t):(await this.whole({signal:t})).filter(a=>pe(a,s));return{records:be(e,ge),total:e.length}}};var B=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function we(n,s){return`${u(n)}#${n.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:n,assemblyName:s,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:i}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,d=we(c,n),g={uniqueId:d,assemblyName:s,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:i,syntenyId:d,mate:{refName:c.contig,start:p,end:l,assemblyName:e}};return new ae(g)}}function Se({pair:n,lane:s,mateLane:t}){return ie({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:s,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:t,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Pe=12e4;function Ne(n,s){let t=new Map;for(let a of n)for(let{name:r,start:o,end:i}of a.walkSpans()){let c=u(r);if(s.has(c)){let p=`${c}#${r.contig}`,l=t.get(p);l?l.push([o,i]):t.set(p,[[o,i]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Pe&&(e=Math.max(e,o))}}return e}function _(n,s){return n instanceof U&&(n.message=`Zoom in to about ${j(n.fitsBp)} to see ${s}`),n}var le=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),D=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await ce(t,this.pluginManager),r=a.location,o=await Z.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await $(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,i),referenceSamples:c});return{db:o,anchor:i,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?ee(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let i=u(o.name),c=r.get(i);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(i,{prefix:i,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a}=await this.graph(t),r=C(this),o=[];for(let i of await this.getHaplotypes(t))i.sample!==a&&o.push({name:q(r,i.prefix),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,lanes:o}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,i=o===a?void 0:P(this,o),c=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),i)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>M(r,a)&&(e===void 0||F(u(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:i,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:d,end:g}=le(t);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${i} has no indexed path ${l} in this graph`);let w=this.keepPredicate(e.haplotypes);if(w!==void 0&&!r.hasHaplotypeIndex)throw new B(c);let f=await X(r,y,d,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:w}).catch(x=>{throw _(x,"the graph")});return typeof f=="string"?f:ne(f,{start:d,end:g},e.walkRows)}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=P(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:i,end:c}=t,p=P(this,e.targetAssemblyName),l=C(this),d=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await I(`Reading graph ${o}:${i.toLocaleString()}-${c.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:i,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:d}).catch(f=>{throw _(z(f,y,c-i)??f,"lanes")})):[]).flatMap(f=>{let x=f.resolved?xe({alignment:f,assemblyName:r,refName:o,lane:q(l,u(f.name))}):void 0;return x===void 0?[]:[x]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:i,end:c}=t,l=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),d=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),w=this.getConf("context"),f=(m,h)=>r.getSubgraphs({path:m,start:i,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>d.has(u(S))}),x=async m=>{let h=await f(m,w).catch(b=>{throw _(z(b,y,c-i)??b,"lanes")}),S=Ne(h,d),R=Math.ceil(S/2)+2e3;return S>0&&R>w?f(m,R).catch(b=>{if(b instanceof W)return h;throw b}):h};return(g&&l.length>0?await I(se(e),a.statusCallback,()=>x(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(b=>R.flatMap(me=>m.pairAlignments({target:b,query:me,bases:!1}).map(fe=>Se({pair:fe,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=le(t);return te(async r=>{let{db:o,anchor:i,unreadableIndex:c}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new B(c);if(a.assemblyName===i){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let d of l)r.next(d)}r.complete()},e.signal)}};export{B as NoHaplotypeIndexError,de as PairTargetError,D as default,Ne as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-3HGD7PKF.js.map

package/dist/chunks/GraphGenomeView-XFKMJK7G.js

@@ -0,0 +1,10 @@
+import{a as C}from"./chunk-QRNPWFVR.js";import"./chunk-5CGGJIAV.js";import"./chunk-QFA7ZXMQ.js";import"./chunk-4R3V6BOH.js";import{h as d}from"./chunk-TWGSFJTO.js";import"./chunk-D4L7BXI7.js";import"./chunk-X7LTMIYL.js";import"./chunk-IPMAQCYX.js";import"./chunk-HYKQBZA4.js";import"./chunk-A7DB4V4C.js";import"./chunk-TFPHVH5H.js";import"./chunk-TVFR5KBQ.js";import"./chunk-Y7UUDKJL.js";import"./chunk-HVBY3TGB.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-KM3QNC77.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as x}from"./chunk-YU7T5WOQ.js";import{A as l,F as L,H as p,e as s,j as v,o as n,x as G}from"./chunk-UGCNPRKC.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),E=i(function({model:e}){let{classes:t}=w();return!e.error&&!e.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage||void 0}),e.canCancelLoad?a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"}):null]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
+S	1	ACGT
+S	2	GGCC
+S	3	TTAA
+S	4	CCGG
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	2	+	4	+	0M
+L	3	+	4	+	0M`,S=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),T=i(function({model:e}){let{classes:t}=S(),[m,M]=x("");function h(){let o=m.trim();o&&e.loadGFAFromLocation({uri:o,locationType:"UriLocation"})}function N(o){let c=o.target.files?.[0];o.target.value="",c&&c.text().then(f=>e.loadGFA(f,c.name)).catch(f=>{e.setError(f)})}return r(l,{className:t.paper,children:[a("div",{className:t.header,children:a(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",a("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:o=>{N(o)}})]}),a(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[a(L,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{M(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&h()},className:t.flex1}),a(n,{variant:"contained",onClick:()=>{h()},disabled:!m.trim(),children:"Open"})]})]}),a("div",{className:t.footer,children:a(n,{size:"small",onClick:()=>{e.loadGFA(F,"Example graph")},children:"Load 4-node example"})}),e.error?a(s,{error:e.error}):null]})}),P=T;var A=i(function({model:e}){return e.hasGraph?a(C,{model:e}):e.canRetryLoad?a(g,{model:e}):r(y,{children:[e.isLoading?a(g,{model:e}):null,a("div",{hidden:e.isLoading,children:a(P,{model:e})})]})}),J=A;export{J as default};
+//# sourceMappingURL=GraphGenomeView-XFKMJK7G.js.map

package/dist/chunks/GraphGenomeView-XFKMJK7G.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/GraphLoadStatus.tsx", "../../src/GraphGenomeView/components/ImportForm.tsx", "../../src/GraphGenomeView/components/GraphGenomeView.tsx"],
+  "sourcesContent": ["import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs or waits on\n// its assembly, and after a load of a source it can retry was canceled or\n// failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (!model.error && !model.loadCanceled) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses\n            variant=\"h6\"\n            message={model.statusMessage || undefined}\n          />\n          {model.canCancelLoad ? (\n            <Button\n              size=\"small\"\n              data-testid=\"graph-genome-cancel\"\n              onClick={() => {\n                model.cancelLoad()\n              }}\n            >\n              Cancel\n            </Button>\n          ) : null}\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    const uri = url.trim()\n    if (uri) {\n      void model.loadGFAFromLocation({ uri, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    // or picking the same file again fires no change\n    event.target.value = ''\n    if (file) {\n      file\n        .text()\n        .then(text => model.loadGFA(text, file.name))\n        .catch((err: unknown) => {\n          model.setError(err)\n        })\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleUrlLoad()\n            }}\n            disabled={!url.trim()}\n          >\n            Open\n          </Button>\n        </div>\n      </div>\n\n      <div className={classes.footer}>\n        <Button\n          size=\"small\"\n          onClick={() => {\n            void model.loadGFA(EXAMPLE_GFA, 'Example graph')\n          }}\n        >\n          Load 4-node example\n        </Button>\n      </div>\n\n      {model.error ? <ErrorBanner error={model.error} /> : null}\n    </Paper>\n  )\n})\n\nexport default ImportForm\n", "import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphPaneModel } from '../model'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it, including while its assembly loads\n  if (model.canRetryLoad) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n"],
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+  "names": ["useStyles", "makeStyles", "GraphLoadStatus", "observer", "model", "classes", "jsxs", "Paper", "jsx", "LoadingEllipses", "Button", "LinearProgress", "ErrorBanner", "Typography", "GraphLoadStatus_default", "EXAMPLE_GFA", "useStyles", "makeStyles", "ImportForm", "observer", "model", "classes", "url", "setUrl", "useState", "handleUrlLoad", "uri", "handleFileUpload", "event", "file", "text", "err", "jsxs", "Paper", "jsx", "Typography", "Button", "TextField", "e", "ErrorBanner", "ImportForm_default", "GraphGenomeView", "observer", "model", "jsx", "GraphCanvas_default", "GraphLoadStatus_default", "jsxs", "Fragment", "ImportForm_default", "GraphGenomeView_default"]
+}

package/dist/chunks/GraphTrackSettingsDialog-4RYY6B25.js

@@ -0,0 +1,6 @@
+import{b as k}from"./chunk-5CGGJIAV.js";import{b as G,c as L}from"./chunk-E2QPSDQL.js";import{h}from"./chunk-TWGSFJTO.js";import"./chunk-IPMAQCYX.js";import"./chunk-HYKQBZA4.js";import"./chunk-Y7UUDKJL.js";import"./chunk-MVVXRZXV.js";import"./chunk-KM3QNC77.js";import"./chunk-5OI6LO4I.js";import{g as x,h as u}from"./chunk-YU7T5WOQ.js";import{D as v,F as y,H as c,n as S,s as b,w as C,z as H}from"./chunk-UGCNPRKC.js";import{b as o,c as l,d as i}from"./chunk-JMBDTNUR.js";var I=h()({section:{marginBottom:24},formControl:{minWidth:200}}),N=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],P=i(function({model:t}){let{classes:p}=I(),a=t.sourceAdapter;return a?.type==="RgfaTabixAdapter"&&!G(a)?l("div",{className:p.section,children:[l(b,{className:p.formControl,children:[o(C,{children:"Graph context"}),o(v,{value:t.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:r=>{t.setSubgraphContext(r.target.value),t.recut()},children:N.map(({value:r,label:e})=>o(H,{value:r,children:e},r))})]}),o(c,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),F=P;var T=h()({section:{marginBottom:24}});function w(n){return n.split(/[\s,]+/).filter(t=>t!=="")}var A=i(function({model:t}){let[p,a]=u(t.cutHaplotypes?.join(", ")??""),r=()=>{let e=w(p);e.join(`
+`)===(t.cutHaplotypes??[]).join(`
+`)||(t.setSubgraphHaplotypes(e),t.recut())};return o(y,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:p,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:e=>{a(e.target.value)},onBlur:()=>{r()},onKeyDown:e=>{e.key==="Enter"&&r()}})}),D=i(function({model:t,names:p}){let[a,r]=u(t.cutHaplotypes??[]),e=x(a),[d,m]=u(!1),g=s=>{s.join(`
+`)!==(t.cutHaplotypes??[]).join(`
+`)&&(t.setSubgraphHaplotypes(s),t.recut())};return o(S,{multiple:!0,freeSolo:!0,autoSelect:!0,disableCloseOnSelect:!0,options:p,value:a,open:d,onOpen:()=>{m(!0)},onClose:()=>{m(!1),g(e.current)},onChange:(s,f)=>{e.current=f,r(f),d||g(f)},renderInput:s=>o(y,{...s,label:"Haplotypes",placeholder:a.length===0?"every haplotype":void 0,slotProps:{...s.slotProps,htmlInput:{...s.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),B=i(function({model:t}){let{classes:p}=T(),a=t.haplotypeNames,r=t.cutHaplotypes?.join(",")??"",e=t.sourceAdapter;return e&&L(e)?l("div",{className:p.section,children:[a?o(D,{model:t,names:a},r):o(A,{model:t},r),l(c,{variant:"caption",component:"div",color:"text.secondary",children:[a?`Which of the graph's ${a.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),M=B;function O({model:n,onClose:t}){return l(k,{model:n,onClose:t,children:[o(F,{model:n}),o(M,{model:n})]})}export{O as default};
+//# sourceMappingURL=GraphTrackSettingsDialog-4RYY6B25.js.map

package/dist/chunks/GraphTrackSettingsDialog-4RYY6B25.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
+  "sourcesContent": ["import {\n  FormControl,\n  InputLabel,\n  MenuItem,\n  Select,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: 0, label: 'None' },\n  { value: 1, label: '1 hop' },\n  { value: 2, label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const adapter = model.sourceAdapter\n  return adapter?.type === 'RgfaTabixAdapter' && !walkIndexed(adapter) ? (\n    <div className={classes.section}>\n      <FormControl className={classes.formControl}>\n        <InputLabel>Graph context</InputLabel>\n        <Select\n          value={model.subgraphContext}\n          label=\"Graph context\"\n          data-testid=\"graph-context-select\"\n          onChange={e => {\n            model.setSubgraphContext(e.target.value)\n            model.recut()\n          }}\n        >\n          {SUBGRAPH_CONTEXTS.map(({ value, label }) => (\n            <MenuItem key={value} value={value}>\n              {label}\n            </MenuItem>\n          ))}\n        </Select>\n      </FormControl>\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useRef, useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nfunction parseHaplotypeList(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft)\n    const unchanged =\n      parsed.join('\\n') === (model.cutHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      model.recut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too, and\n// becomes a chip on blur as well as on Enter. The set applies when the list\n// closes or, with the list closed, as it changes. The ref holds the draft\n// because a blur's onChange and onClose land in one event, before a rerender.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const draftRef = useRef(draft)\n  const [open, setOpen] = useState(false)\n  const apply = (haplotypes: string[]) => {\n    if (haplotypes.join('\\n') !== (model.cutHaplotypes ?? []).join('\\n')) {\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      autoSelect\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onClose={() => {\n        setOpen(false)\n        apply(draftRef.current)\n      }}\n      onChange={(_, value) => {\n        draftRef.current = value\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set. The inner field is\n// keyed on it so an outside change (a restored session, a launch) resets the\n// draft rather than fighting it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const key = model.cutHaplotypes?.join(',') ?? ''\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField key={key} model={model} names={names} />\n      ) : (\n        <HaplotypeListField key={key} model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
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+  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "FormControl", "jsx", "InputLabel", "Select", "e", "value", "label", "MenuItem", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "HaplotypeListField", "observer", "model", "draft", "setDraft", "useState", "apply", "parsed", "jsx", "TextField", "HaplotypePickField", "names", "draftRef", "useRef", "open", "setOpen", "haplotypes", "Autocomplete", "_", "value", "params", "SubgraphHaplotypesField", "classes", "key", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
+}

package/dist/chunks/LinearGraphDisplay-GLJ3L2IZ.js

@@ -0,0 +1,2 @@
+import{a as g}from"./chunk-QRNPWFVR.js";import"./chunk-5CGGJIAV.js";import"./chunk-QFA7ZXMQ.js";import"./chunk-4R3V6BOH.js";import"./chunk-TWGSFJTO.js";import"./chunk-D4L7BXI7.js";import"./chunk-X7LTMIYL.js";import"./chunk-IPMAQCYX.js";import"./chunk-HYKQBZA4.js";import"./chunk-A7DB4V4C.js";import"./chunk-TFPHVH5H.js";import"./chunk-TVFR5KBQ.js";import"./chunk-Y7UUDKJL.js";import"./chunk-HVBY3TGB.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-KM3QNC77.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as y}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as e,c as l,d as T}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var v=s&&s.__esModule?s.default:s;var i=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var h=i&&i.__esModule?i.default:i;var a=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=a&&a.__esModule?a.default:a;var n=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var f=n&&n.__esModule?n.default:n;var t=JBrowseExports["@jbrowse/display-ui"],p=r=>t!=null&&r in Object(t)?t[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=p("BottomRightCornerContext");var c=p("TrackOverlayPortal");var L=p("useChromeOverlayOverride");var j=t&&t.__esModule?t.default:t;var D={TooLarge:f,ErrorBar:h,Loading:O,BackgroundProgress:v};function d({model:r,phase:o,drawn:u,testid:_,style:C,children:E,...B}){let{TooLarge:G,ErrorBar:S,Loading:b,BackgroundProgress:m}=L()??D,[P,A]=y(null),x={...B,"data-testid":_,"data-display-id":r.configuration.displayId,"data-display-drawn":u,"data-display-phase":o};return o==="tooLarge"?e("div",{style:{display:"contents"},...x,children:e(c,{children:e("div",{style:{pointerEvents:"auto"},children:e(G,{model:r})})})}):l("div",{style:{position:"relative",height:r.height,...C},...x,children:[e(w,{value:P,children:E}),l(c,{children:[e(S,{model:r,visible:o==="error"}),e(b,{model:r,visible:o==="loading"||o==="canceled",immediate:!u}),e("div",{ref:A,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:e(m,{model:r,visible:o==="ready"})})]})]})}var I=T(function({model:o}){return e(d,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(g,{model:o,ownChrome:!1})})}),Q=I;export{Q as default};
+//# sourceMappingURL=LinearGraphDisplay-GLJ3L2IZ.js.map

package/dist/chunks/{LinearGraphDisplay-QYPXZEX7.js.map → LinearGraphDisplay-GLJ3L2IZ.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["host:@jbrowse/display-kit/DisplayBackgroundProgress", "host:@jbrowse/display-kit/DisplayErrorBar", "host:@jbrowse/display-kit/DisplayLoadingOverlay", "host:@jbrowse/display-kit/TooLargeMessage", "host:@jbrowse/display-ui", "../../src/LinearGraphDisplay/components/GraphStatusChrome.tsx", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
   "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/DisplayBackgroundProgress\"]\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 '\" + \"@jbrowse/display-kit/DisplayBackgroundProgress\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayErrorBar\"]\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 '\" + \"@jbrowse/display-kit/DisplayErrorBar\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayLoadingOverlay\"]\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 '\" + \"@jbrowse/display-kit/DisplayLoadingOverlay\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/TooLargeMessage\"]\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 '\" + \"@jbrowse/display-kit/TooLargeMessage\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-ui\"]\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 '\" + \"@jbrowse/display-ui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const AXIS_GUTTER_WIDTH_PX = /* @__PURE__ */ read(\"AXIS_GUTTER_WIDTH_PX\")\nexport const AXIS_RIGHT_INSET_PX = /* @__PURE__ */ read(\"AXIS_RIGHT_INSET_PX\")\nexport const AxisCaption = /* @__PURE__ */ read(\"AxisCaption\")\nexport const AxisCaptionOverlay = /* @__PURE__ */ read(\"AxisCaptionOverlay\")\nexport const AxisGutter = /* @__PURE__ */ read(\"AxisGutter\")\nexport const BOTTOM_RIGHT_CONTROLS_ORDER = /* @__PURE__ */ read(\"BOTTOM_RIGHT_CONTROLS_ORDER\")\nexport const BottomRightCornerContext = /* @__PURE__ */ read(\"BottomRightCornerContext\")\nexport const COMPACT_AXIS_HEIGHT = /* @__PURE__ */ read(\"COMPACT_AXIS_HEIGHT\")\nexport const CrossHatchLines = /* @__PURE__ */ read(\"CrossHatchLines\")\nexport const CrossHatches = /* @__PURE__ */ read(\"CrossHatches\")\nexport const DEFAULT_RULE_COLOR = /* @__PURE__ */ read(\"DEFAULT_RULE_COLOR\")\nexport const DisplayChromeOverlayProvider = /* @__PURE__ */ read(\"DisplayChromeOverlayProvider\")\nexport const DisplayUIProvider = /* @__PURE__ */ read(\"DisplayUIProvider\")\nexport const FLOATING_LEGEND_RIGHT_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_RIGHT_PX\")\nexport const FLOATING_LEGEND_TOP_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_TOP_PX\")\nexport const FloatingLegend = /* @__PURE__ */ read(\"FloatingLegend\")\nexport const FloatingSvgOverlay = /* @__PURE__ */ read(\"FloatingSvgOverlay\")\nexport const FloatingText = /* @__PURE__ */ read(\"FloatingText\")\nexport const PointerLayer = /* @__PURE__ */ read(\"PointerLayer\")\nexport const SCORE_CAPTION_HEIGHT = /* @__PURE__ */ read(\"SCORE_CAPTION_HEIGHT\")\nexport const ScoreDomainCaption = /* @__PURE__ */ read(\"ScoreDomainCaption\")\nexport const ScoreRuleLines = /* @__PURE__ */ read(\"ScoreRuleLines\")\nexport const ScoreRules = /* @__PURE__ */ read(\"ScoreRules\")\nexport const SvgHaloText = /* @__PURE__ */ read(\"SvgHaloText\")\nexport const TEXT_BASELINE_RATIO = /* @__PURE__ */ read(\"TEXT_BASELINE_RATIO\")\nexport const Tooltip = /* @__PURE__ */ read(\"Tooltip\")\nexport const TrackControlProvider = /* @__PURE__ */ read(\"TrackControlProvider\")\nexport const TrackOverlayContext = /* @__PURE__ */ read(\"TrackOverlayContext\")\nexport const TrackOverlayPortal = /* @__PURE__ */ read(\"TrackOverlayPortal\")\nexport const TrackOverlaySlot = /* @__PURE__ */ read(\"TrackOverlaySlot\")\nexport const YSCALEBAR_LABEL_OFFSET = /* @__PURE__ */ read(\"YSCALEBAR_LABEL_OFFSET\")\nexport const YScaleBar = /* @__PURE__ */ read(\"YScaleBar\")\nexport const YScaleBarOverlay = /* @__PURE__ */ read(\"YScaleBarOverlay\")\nexport const axisDrawn = /* @__PURE__ */ read(\"axisDrawn\")\nexport const axisGutterLeft = /* @__PURE__ */ read(\"axisGutterLeft\")\nexport const axisGutterWidth = /* @__PURE__ */ read(\"axisGutterWidth\")\nexport const axisPlotBox = /* @__PURE__ */ read(\"axisPlotBox\")\nexport const clampStrokeInsideAxis = /* @__PURE__ */ read(\"clampStrokeInsideAxis\")\nexport const cullOverlappingLabels = /* @__PURE__ */ read(\"cullOverlappingLabels\")\nexport const formatScore = /* @__PURE__ */ read(\"formatScore\")\nexport const isLiveModel = /* @__PURE__ */ read(\"isLiveModel\")\nexport const leftAxisGutterWidth = /* @__PURE__ */ read(\"leftAxisGutterWidth\")\nexport const plainChromeOverlays = /* @__PURE__ */ read(\"plainChromeOverlays\")\nexport const plainTrackControl = /* @__PURE__ */ read(\"plainTrackControl\")\nexport const resolveOverlays = /* @__PURE__ */ read(\"resolveOverlays\")\nexport const scoreToAxisY = /* @__PURE__ */ read(\"scoreToAxisY\")\nexport const textHalo = /* @__PURE__ */ read(\"textHalo\")\nexport const tooLargeBannerText = /* @__PURE__ */ read(\"tooLargeBannerText\")\nexport const useChromeOverlayOverride = /* @__PURE__ */ read(\"useChromeOverlayOverride\")\nexport const useTooltip = /* @__PURE__ */ read(\"useTooltip\")\nexport const useTrackControlMenu = /* @__PURE__ */ read(\"useTrackControlMenu\")\nexport const useTrackControlOverride = /* @__PURE__ */ read(\"useTrackControlOverride\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\nimport type { CSSProperties, ReactNode } from 'react'\n\nimport DisplayBackgroundProgress from '@jbrowse/display-kit/DisplayBackgroundProgress'\nimport DisplayErrorBar from '@jbrowse/display-kit/DisplayErrorBar'\nimport DisplayLoadingOverlay from '@jbrowse/display-kit/DisplayLoadingOverlay'\nimport TooLargeMessage from '@jbrowse/display-kit/TooLargeMessage'\nimport {\n  BottomRightCornerContext,\n  TrackOverlayPortal,\n  useChromeOverlayOverride,\n} from '@jbrowse/display-ui'\n\nimport type { LinearGraphDisplayModel } from '../model'\nimport type { DisplayStatusPhase } from '@jbrowse/render-core/displayPhase'\n\nconst muiOverlays = {\n  TooLarge: TooLargeMessage,\n  ErrorBar: DisplayErrorBar,\n  Loading: DisplayLoadingOverlay,\n  BackgroundProgress: DisplayBackgroundProgress,\n}\n\n/**\n * The status chrome of a display that owns its canvas: the zoom-in notice in\n * place of the display, and the error bar, loading overlay and progress chip\n * over it in the track's overlay layer. Core's `DisplayStatusChrome` drew this\n * until jbrowse-web main removed it on 2026-10-08 (d8db736896), and its named\n * import came back undefined there, failing the track with React error #130.\n * Built here from the overlays every host from 5.0.0-beta.11 serves.\n */\nexport default function GraphStatusChrome({\n  model,\n  phase,\n  drawn,\n  testid,\n  style,\n  children,\n  ...dataProps\n}: {\n  model: LinearGraphDisplayModel\n  phase: DisplayStatusPhase\n  drawn: boolean\n  testid: string\n  style?: CSSProperties\n  children: ReactNode\n} & Record<`data-${string}`, unknown>) {\n  const { TooLarge, ErrorBar, Loading, BackgroundProgress } =\n    useChromeOverlayOverride() ?? muiOverlays\n  const [corner, setCorner] = useState<HTMLDivElement | null>(null)\n  const attributes = {\n    ...dataProps,\n    'data-testid': testid,\n    'data-display-id': model.configuration.displayId,\n    'data-display-drawn': drawn,\n    'data-display-phase': phase,\n  }\n  if (phase === 'tooLarge') {\n    return (\n      <div style={{ display: 'contents' }} {...attributes}>\n        <TrackOverlayPortal>\n          <div style={{ pointerEvents: 'auto' }}>\n            <TooLarge model={model} />\n          </div>\n        </TrackOverlayPortal>\n      </div>\n    )\n  }\n  return (\n    <div\n      style={{ position: 'relative', height: model.height, ...style }}\n      {...attributes}\n    >\n      <BottomRightCornerContext value={corner}>\n        {children}\n      </BottomRightCornerContext>\n      <TrackOverlayPortal>\n        <ErrorBar model={model} visible={phase === 'error'} />\n        <Loading\n          model={model}\n          visible={phase === 'loading' || phase === 'canceled'}\n          immediate={!drawn}\n        />\n        <div\n          ref={setCorner}\n          style={{\n            position: 'absolute',\n            bottom: 2,\n            right: 2,\n            display: 'flex',\n            flexDirection: 'column',\n            alignItems: 'flex-end',\n            gap: 4,\n            pointerEvents: 'none',\n          }}\n        >\n          <BackgroundProgress model={model} visible={phase === 'ready'} />\n        </div>\n      </TrackOverlayPortal>\n    </div>\n  )\n}\n", "import { observer } from 'mobx-react'\n\nimport GraphStatusChrome from './GraphStatusChrome'\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <GraphStatusChrome\n      model={model}\n      phase={model.displayPhase}\n      drawn={model.painted && model.geometryPainted}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? 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e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?tn(e.chosenLayoutMode,e.graph):!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?Ae(t):[]},get effectiveDrawPaths(){return e.drawPaths&&tt(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){let t=e.openBubbles.at(-1);return t&&!t.offReference&&t.end>t.start?{start:t.start,end:t.end}:e.statedColorDomain??e.graphRegion},get drawnReferenceRamp(){let t=e.drawnGraph;return t?Ge(t,this.rampDomain):void 0},get walkRamp(){return e.walkLayers.some(t=>t.color?.field==="reference")?this.drawnReferenceRamp:void 0},get modeDrawsNodes(){return Y(e.chosenLayoutMode).drawsNodes},get liftedWalkLayers(){return e.walkLayers.length>0||!this.modeDrawsNodes?e.walkLayers:e.hoveredRowWalks.map(t=>({walk:t}))},get walkLift(){let{graph:t}=e,n=this.liftedWalkLayers;return t&&!e.walkCut&&n.length>0&&!e.layoutResult?.tubeMap?je(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facetSetting.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?Ye(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!so.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return nt(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){for(let t of this.walkLift?.walks??[])if(t.encoding.field!=="walk"){for(let n of t.colors.values())if(n===to)return!0}return!1},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":ze(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?Mt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>Mt(Ke(t,le(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(le(t)),s=new Set(n.nodes.filter(a=>o.has(a.name)).map(a=>a.id)),r=new Set;return n.edges.forEach((a,i)=>{s.has(a.from)&&s.has(a.to)&&r.add(i)}),{walks:[],nodeIds:s,edgeIndexes:r,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>ft(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,s=this.openBubbleFocus;return o?!n.some(r=>o.nodeIds.has(r)):!!s&&!this.bubbleIsOpen(t)&&!n.every(r=>s.nodeIds.has(r))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new 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t=e.containingView;if(!t)return;let n=jo(t,e.geneTrack?.trackId);return n.length?new Fr({filters:n,jexl:Nn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Yo(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,s=e.drawsLoadedReference||n!==void 0&&Ct(t,[n])!==void 0;return t&&o&&s?Ot(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?ge(e.drawnGraph):void 0},get nodeInk(){return ot(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?Ne(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?fa(n,t,t.unit):ye(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[s,...r]=zo([o.reference,...o.rows],t?.calls);return{...o,reference:s,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&Tn(t)?t:void 0},get walkRowGroupFields(){return wo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Mo(t,n),s=(e.graph?.paths??[]).map(r=>O(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Ro(s.map(o)),unvalued:s.some(r=>o(r)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows;return t&&$e(t.rows,e.walkRowSamples)},get walkRowGroups(){let 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screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Pe(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,o=n?.tubeMap?n.nodePositions:void 0,s=!1,r=!1;if(t&&e.drawnGraph)for(let a of e.drawnGraph.nodes)o&&!o[a.id]||(t.midpoints.has(a.id)?a.stable&&a.stable.rank>0&&(s=!0):r=!0);return{offReference:s,unplaced:r}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?xn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!tt(n.length)||n.some(s=>s.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],s=this.tubeColorKind,r=e.tubeMapColoring;return s==="value"&&r?vo(o,t.referencePath,r.valueOf,r.palette):s==="tinted"?Kt(o,t.referencePath,So):s==="role"?Kt(o,t.referencePath):n},fadeUnhovered(t,n,o){let s=new Set(e.hoveredRowWalks);return s.size>0?t.map((r,a)=>{let i=n[a]?.name??"";return s.has(i)||o!==void 0&&O(i).name===o?r:rt}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return Ur(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&zr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&ge(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&tt(t.length)&&!t.some(o=>o.members)?Ae(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?Ur(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var qr=Kr.views(e=>({get host(){let t=e.containingView;return Sr(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?ee(t):[];return 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