jbrowse-plugin-graphgenomeviewer 7.1.7 → 7.1.9

package/dist/chunks/chunk-37IAMKOU.js

@@ -0,0 +1,3 @@
+import{b as Qn,g as Vo,h as jo,j as bt,k as wt,l as Yo,m as zo}from"./chunk-RROZDQ35.js";import{$ as ut,$b as gt,A as qn,Aa as we,B as Jn,Ba as lo,C as Zn,Ca as po,Cb as No,D as at,E as Dt,Ea as uo,Eb as Po,Fa as fo,Fb as qt,Gb as Ao,Hb as To,I as Xt,Ia as le,J as it,Ja as ho,Jb as Go,L as Vt,M as Ee,Mb as oe,N as ct,O as J,Ob as Io,P as dt,Pb as Eo,Qb as Co,R as lt,Ra as go,Rb as Oo,S as pt,Sb as Bo,Tb as _o,U as jt,Ub as $o,Vb as Wo,W,Wa as bo,Xb as Fo,Yb as Ho,Z as Ce,Zb as Do,_ as Oe,_b as Xo,aa as eo,b as In,bb as wo,bc as Uo,cc as Ko,d as _t,db as yo,e as Qe,ea as oo,eb as ko,f as En,fa as mt,fb as xo,g as Cn,ga as ro,gb as So,h as On,i as Bn,ia as so,ja as ao,l as Vn,lb as Ro,m as Ht,n as Te,ob as Kt,qb as vo,ra as io,rb as Mo,s as Ie,sb as Lo,t as ne,ta as co,u as de,ua as Ut,xa as Be,y as Kn}from"./chunk-4OUZ2RST.js";import{a as ge,b as $t,d as jn,f as Yn,i as rt,m as Ge,n as zn,o as Un,p as st,s as Yt,t as to,u as no,v as zt}from"./chunk-X7LTMIYL.js";import{B as Ne,C as Pe,D as Fn,F as Hn,O as tt,P as Dn,Q as Xn,R as Ae,S as nt,W as ot,a as U,d as O,i as _n,j as Me,k as be,l as Wt,n as $n,o as Wn,p as Le,t as et,u as ce,z as Ft}from"./chunk-HYKQBZA4.js";import{b as ft,c as ht,e as mo}from"./chunk-A7DB4V4C.js";import{b as It,c as Et,d as Ct,f as Ot}from"./chunk-TFPHVH5H.js";import{b as he,c as E,d as Re,e as ee,f as At,g as ie,h as Tt,i as Gt,j as ve}from"./chunk-Y7UUDKJL.js";import{c as Gn,d as Bt}from"./chunk-HVBY3TGB.js";import{c as An,e as X}from"./chunk-MVVXRZXV.js";import{a as Ze,c as Pn,d as fe}from"./chunk-KM3QNC77.js";import{d as Tn}from"./chunk-IKJZPPOA.js";import{f as Ln,g as Pt,h as Nn,j as q}from"./chunk-TENPGIPX.js";import{b as j}from"./chunk-JMBDTNUR.js";var pe=JBrowseExports["@mui/material/SvgIcon"],is=e=>pe!=null&&e in Object(pe)?pe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@mui/material/SvgIcon' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),V=is("createSvgIcon"),Ia=pe&&pe.__esModule?pe.default:pe;var cs=/^[^#]+#\d+$/;function ds(e,t){let n=e.assemblyNameToPanSN??{},o=new Set(Object.values(n)),s={};for(let{name:r,aliases:a}of t){let i=a.find(c=>cs.test(c));i!==void 0&&!o.has(i)&&(s[r]=i)}return Object.keys(s).length===0?e:{...e,assemblyNameToPanSN:{...s,...n}}}function ls(e,t){let n=a=>t.find(i=>i.name===a||i.aliases.includes(a))?.name??a,o=e.assemblyNames??[],s=e.assemblyNameToPanSN??{};if([...o,...Object.keys(s)].every(a=>n(a)===a))return e;let r=new Map;for(let[a,i]of Object.entries(s)){let c=n(a);(c===a||!r.has(c))&&r.set(c,i)}for(let a of o){let i=n(a);i!==a&&!r.has(i)&&r.set(i,a)}return{...e,assemblyNames:o.map(n),assemblyNameToPanSN:Object.fromEntries(r)}}var ps=new Set(["GbzBaseSyntenyAdapter","WalkTabixSyntenyAdapter"]);function qo(e,t){let n=X(t,"adapter");if(!ps.has(n.type)&&!Qn(n))return n;let o=q(e).assemblyManager.assemblyList.map(s=>({name:X(s,"name"),aliases:X(s,"aliases")??[]}));return ds(ls(n,o),o)}var us=1,ms=.015;function yt({graph:e,span:t,rowY:n,positions:o}){let s=t*ms,r=En(e),a=new Map(e.nodes.map(u=>[u.id,u])),i=[];for(let u of r){let p=u.refSpan-u.pathLength;p>=us&&i.push({nodeIds:u.nodeIds,bp:p});let d=Math.max(u.refSpan,s),m=u.pathLength>0?d/u.pathLength:0;u.nodeIds.forEach((f,b)=>{let g=a.get(f);if(g){let w=u.nodeOffsets[b],S=d/u.nodeIds.length,x=k=>u.start+k*m,h=n(g);o[f]=m?[{x:x(w),y:h},{x:x(w+g.length),y:h}]:[{x:u.start+b*S,y:h},{x:u.start+(b+1)*S,y:h}]}})}let c=ge(e),l=Object.keys(o);for(let u of l){let p=o[u].at(-1).x;for(let d of c.get(u)??[]){let m=a.get(d);if(m&&!(d in o)){let f=n(m);o[d]=[{x:p,y:f},{x:p+s,y:f}],l.push(d)}}}return i}function fs(e,t){let n=new Map;for(let s of e.nodes)if(Re(s)){let{sample:r}=Qe(s.stable.refName);n.set(r,(n.get(r)??0)+s.length)}let o=new Map(t.map((s,r)=>[s,r]));return[...n.keys()].sort((s,r)=>(o.get(s)??1/0)-(o.get(r)??1/0)||n.get(r)-n.get(s)||s.localeCompare(r))}function Jo(e,t,n=[]){let o=ee(e),s=fs(e,n);if(o.length===0||s.length===0)return;let r=ve(o,t),a=new Map(s.map((d,m)=>[d,m+1])),i=ie(o),c=s.length+1,l=yt({graph:e,span:r,rowY:d=>{let m=d.stable;return((m?a.get(Qe(m.refName).sample):void 0)??c)*U},positions:i}),p=[{label:Qe(o[0].stable.refName).sample,y:0},...s.map(d=>({label:d,y:a.get(d)*U}))];return{nodePositions:i,rowLabels:p,sampleRows:s,referenceAxis:!0,pixelRows:!0,alleleDeletions:l}}function hs(e){let t=new Map(e.nodes.map(s=>[s.id,s])),n=e.pathVisits,o=n?.replay();return(e.paths??[]).map(s=>{let r=n?.pathIndex(O(s.name).name)??-1;return s.nodeIds.flatMap(a=>{let i=t.get(a);if(!i)return[];let c=n&&o?o(n.slot(i.name),r):-1;return[{node:i,strand:c>=0?n.strand(c):Cn(i)}]})})}function gs(e){let t=hs(e),n=(e.paths??[]).flatMap((s,r)=>{let a=t[r].map(i=>On(i.node,i.strand));return a.length>0?[{id:r,name:s.name,sequence:a,sourceTrackID:0,type:"haplotype",...s.members?{freq:s.members.length}:{}}]:[]}),o=n.findIndex(s=>O(s.name).name===e.referencePath);return o>0&&n.unshift(...n.splice(o,1)),n}function bs(e){return e.nodes.map(t=>({name:t.id,seq:"",sequenceLength:Math.max(1,t.length)}))}function _e(e){return(e.paths?.length??0)>0}var ws=600,ys=3,ks=15;function xs(e){return Math.max(ys,Math.min(ks,Math.floor(ws/Math.max(1,e))))}function Ss(e){let t=new Set,n=new Set;for(let o of e?.sequence??[])Ht(o)?n.has(Te(o))||t.add(Te(o)):n.add(o);return t}function Rs(e,t,n){let o=Ss(n[0]),s=new Map;for(let{sequence:c,is_secondary:l}of n)l||c.forEach((u,p)=>{let d=Te(u),f=Ht(u)!==o.has(d)?c[p+1]:c[p-1];!t.nodeMap.has(d)&&f!==void 0&&s.set(d,Te(f))});let r=new Map(e.nodes.map(c=>[c.id,Math.max(1,c.length)])),a=new Map([...s].map(([c,l])=>[l,c])),i=new Map;for(let c of a.keys()){let l=t.nodeMap.get(c);if(l!==void 0){let u=[c];for(let d=a.get(c);d!==void 0;d=a.get(d))u.push(d);u.reduce((d,m)=>d+(r.get(m)??0),0)===t.nodes[l].sequenceLength&&i.set(c,u)}}return{members:i,flipped:o}}var vs={start:"end",end:"start"},Zo={"+":"-","-":"+"};function Ms(e,{members:t,flipped:n}){if(t.size===0)return e;let o=new Map(e.nodes.map(d=>[d.id,d])),s=new Map,r=new Set,a=(d,m)=>n.has(d)?vs[m]:m;for(let[d,m]of t)m.forEach((f,b)=>{s.set(f,d);let g=m[b+1];g!==void 0&&r.add(`${f}:${a(f,"end")}	${g}:${a(g,"start")}`)});let i=new Set([...s].filter(([d,m])=>d!==m).map(([d])=>d)),c=e.nodes.flatMap(d=>{let m=t.get(d.id);if(!m)return i.has(d.id)?[]:[d];let f=m.map(g=>o.get(g)),b=f.flatMap(g=>g.stable?[g.stable.start]:[]);return[{...d,length:f.reduce((g,w)=>g+w.length,0),stable:d.stable&&{...d.stable,start:Math.min(...b)}}]}),l=(d,m,f)=>a(m,a(d,f))==="end"?et(m):Zo[et(m)],u=e.edges.flatMap(d=>{let m=ce(d),f=`${d.from}:${m.from}`,b=`${d.to}:${m.to}`;if(r.has(`${f}	${b}`)||r.has(`${b}	${f}`))return[];let g=s.get(d.from),w=s.get(d.to);return[{...d,...g===void 0?{}:{from:g,fromStrand:l(d.from,g,m.from)},...w===void 0?{}:{to:w,toStrand:Zo[l(d.to,w,m.to)]}}]}),p=new Set([...i].map(d=>o.get(d)?.name??d));return{...e,nodes:c,edges:u,paths:e.paths?.map(d=>({...d,nodeIds:d.nodeIds.filter(m=>!i.has(m))})),pathVisits:e.pathVisits?.filter(()=>!0,d=>!p.has(d))}}function Qo(e){let t=e.paths??[],n=gs(e),o=e.reads?Bn(e,e.reads,t.length):[],s=o.length>0?Xn:Dn,r=t.map((u,p)=>s(p,t.length)),a=t.some(u=>u.members),i=t.reduce((u,p)=>u+(p.members?.length??1),0),c=Vn(bs(e),n,o,{nodeWidthOption:"compressed",trackWidth:xs(a?i:n.length),...a?{freqWidth:"linear"}:{}});if(!c)return;let l=Rs(e,c,[...n,...o]);return{layout:c,pathColors:r,members:l.members,graph:Ms(e,l)}}function Jt(e){let t=[];return e.nodes.forEach(n=>{n.order>=0&&t.push(n)}),t}function er(e,t,n,o){let s=e.y+e.contentHeight/2-t;return[{x:n,y:s},{x:o,y:s}]}function tr(e,t){return{minY:e.bounds.minY-t,maxY:e.bounds.maxY-t}}function nr(e){let t=_e(e)?Qo(e):void 0;if(!t)return;let{layout:n,...o}=t,s=n.bounds.minY,r={};for(let c of Jt(n))r[c.name]=er(c,s,c.x,c.x+c.pixelWidth);let{minY:a,maxY:i}=tr(n,s);return{nodePositions:r,tubeMap:{layout:n,yOffset:s,...o},extent:{minX:n.bounds.minX,maxX:n.bounds.maxX,minY:a,maxY:i}}}function Ls(e,t){let n=new Map(e.nodes.map(i=>[i.id,i])),o=new Map;for(let i of Jt(t)){let c=o.get(i.order);c?c.push(i):o.set(i.order,[i])}let s=[],r=-1/0;for(let i of[...o.keys()].sort((c,l)=>c-l)){let c=o.get(i),l=1/0,u=-1/0;for(let p of c){let d=n.get(p.name);d&&E(d)&&(l=Math.min(l,d.stable.start),u=Math.max(u,d.stable.start+d.length))}l===1/0&&(l=u=r),l<r&&(l=r,u=Math.max(r,u)),r=Math.max(r,u),s.push({order:i,x0:Math.min(...c.map(p=>p.x)),x1:Math.max(...c.map(p=>p.x+p.pixelWidth)),bp0:l,bp1:u})}let a=s.find(i=>i.bp0!==-1/0);for(let i of s)i.bp0===-1/0&&(i.bp0=i.bp1=a?.bp0??0);return s}function kt(e){return _e(e)&&e.nodes.some(E)}function or(e){let t=kt(e)?Qo(e):void 0;if(!t)return;let{layout:n,...o}=t,s=Ls(o.graph,n),r=new Map(s.map(c=>[c.order,c])),a=n.bounds.minY,i={};for(let c of Jt(n)){let l=r.get(c.order);i[c.name]=er(c,a,l.bp0,l.bp1)}return{nodePositions:i,tubeMap:{layout:n,yOffset:a,columns:s,...o},referenceAxis:!0,pixelRows:!0,extent:tr(n,a)}}function Ns(e){let t=new Set;for(let n of e.nodes)n.stable&&t.add(n.stable.rank);return new Map([...t].sort((n,o)=>n-o).map((n,o)=>[n,o]))}function rr(e,t){let n=ee(e);if(n.length===0)return;let o=ve(n,t),s=Ns(e),r=ie(n),a=yt({graph:e,span:o,rowY:c=>(c.stable?s.get(c.stable.rank)??s.size:s.size)*U,positions:r}),i=[...s].map(([c,l])=>({label:c===0?"Reference (rank 0)":`Rank ${c}`,y:l*U}));return{nodePositions:r,rowLabels:i,referenceAxis:!0,pixelRows:!0,alleleDeletions:a}}var Ps=12,Zt=U;function sr(e){return 10+8*Math.log2(1+e.length)}function re(e,t){return e<t?-1:e>t?1:0}function ir(e,t){return re(e.at,t.at)||re(e.side,t.side)||re(e.hops,t.hops)}var ar={at:1/0,side:0,hops:0};function Qt(e){let t=new Map(e.nodes.map(o=>[o.id,o])),n=Gs(e);return e.nodes.map(o=>o.id).sort((o,s)=>ir(n.get(o)??ar,n.get(s)??ar)||re(t.get(o).name,t.get(s).name)||re(o,s))}function As(e,t){let n=new Set(e.nodes.map(u=>u.id)),o=new Map(t.map(u=>[u.id,u.stable.start])),s=new Map,r=new Map;t.forEach((u,p)=>{r.set(u.id,t[p-1]?.id),s.set(u.id,t[p+1]?.id)});let a=t[0]?.id,i=(u,p)=>{let d=s.get(u);s.set(u,p),r.set(p,u),s.set(p,d),d!==void 0&&r.set(d,p)},c=(u,p)=>{let d=r.get(u);d===void 0?(a=p,r.set(p,void 0),s.set(p,u),r.set(u,p)):i(d,p)};for(let u of e.paths??[]){let p=0,d=0,m;for(let w of u.nodeIds){let S=o.get(w);S!==void 0&&(m!==void 0&&S!==m&&(S>m?p++:d++),m=S)}let f=d>p?[...u.nodeIds].reverse():u.nodeIds,b,g=new Set;for(let w of f)if(s.has(w)){if(b===void 0)for(let S of g)c(w,S);b=w}else n.has(w)&&(b===void 0?g.add(w):(i(b,w),b=w))}let l=[];for(let u=a;u!==void 0;u=s.get(u))l.push(u);return l}function Ts(e,t){let n=[...t.entries()].sort(([a,i],[c,l])=>ir(i,l)||re(a,c)).map(([a])=>a),o=n.length;for(let a of n){let i=t.get(a);for(let c of e.get(a)??[])t.has(c)||(t.set(c,{at:i.at,side:1,hops:i.hops+1}),n.push(c))}let s=new Set(n.slice(o)),r=new Set;for(let a of s){if(r.has(a))continue;let{at:i}=t.get(a),c=[a];r.add(a);let l=!0;for(let u of c){let{hops:p}=t.get(u),d=!0,m=!1;for(let f of e.get(u)??[]){let b=t.get(f);b.at===i&&s.has(f)?(d&&=b.hops<=p,r.has(f)||(r.add(f),c.push(f))):b.at!==i&&(m||=b.at<i,l&&=b.at<i)}l&&=!d||m}if(l)for(let u of c){let p=t.get(u);t.set(u,{...p,side:-1,hops:-p.hops})}}}function Gs(e){let t=new Set(e.nodes.map(r=>r.id)),n=new Map;for(let r of e.edges)!t.has(r.from)||!t.has(r.to)||((n.get(r.from)??n.set(r.from,[]).get(r.from)).push(r.to),(n.get(r.to)??n.set(r.to,[]).get(r.to)).push(r.from));let o=e.nodes.filter(E).sort((r,a)=>re(r.stable.start,a.stable.start)||re(r.name,a.name)),s=new Map;return As(e,o).forEach((r,a)=>{s.set(r,{at:a,side:0,hops:0})}),Ts(n,s),s}function Is(e){let t=new Map(e.nodes.map(p=>[p.id,p])),n=Qt(e),o=new Map(n.map((p,d)=>[p,d])),s=p=>E(t.get(p)),r=new Map(n.map(p=>[p,[]])),a=new Map(n.map(p=>[p,[]])),i=(p,d)=>{r.get(d).push(p),a.get(p).push(d)};for(let p of e.edges)p.from===p.to||!o.has(p.from)||!o.has(p.to)||(o.get(p.from)<o.get(p.to)?i(p.from,p.to):i(p.to,p.from));let c=n.filter(s);for(let p=1;p<c.length;p++)i(c[p-1],c[p]);let l=new Map;for(let p of n){let d=0;for(let m of r.get(p))d=Math.max(d,l.get(m)+1);l.set(p,d)}for(let p=n.length-1;p>=0;p--){let d=n[p],m=a.get(d);if(s(d)||m.length===0)continue;let f=1/0;for(let w of m)f=Math.min(f,l.get(w));let b=l.get(d),g=Math.max(b,f-1);l.set(d,Math.floor((b+g)/2))}let u=[];for(let p of n)(u[l.get(p)]??=[]).push(p);return{layers:u,layerOf:l,preds:r}}function cr(e){if(!e.nodes.some(E))return;let t=new Map(e.nodes.map(p=>[p.id,p])),n=p=>E(t.get(p)),{layers:o,layerOf:s,preds:r}=Is(e),a=o.map(p=>{let d=0;for(let m of p)d=Math.max(d,sr(t.get(m)));return d}),i=[],c=0;for(let p=0;p<o.length;p++)i[p]=c,c+=a[p]+Ps;let l=new Map;for(let p of o){let d=[];for(let f of p){if(n(f)){l.set(f,0);continue}let b=r.get(f).filter(w=>l.has(w)),g=0;for(let w of b)g+=l.get(w)/b.length;d.push({id:f,ideal:g===0?Zt:g})}d.sort((f,b)=>f.ideal-b.ideal);let m=new Set([0]);for(let{id:f,ideal:b}of d){let g=Math.round(b/Zt);g===0&&(g=b>=0?1:-1);for(let w=1;m.has(g);w++)m.has(g+w)?m.has(g-w)||(g-=w):g+=w;m.add(g),l.set(f,g*Zt)}}let u={};for(let p of e.nodes){let d=s.get(p.id),m=sr(p),f=i[d]+a[d]/2,b=l.get(p.id);u[p.id]=[{x:f-m/2,y:b},{x:f+m/2,y:b}]}return{nodePositions:u,referenceAxis:!1,pixelRows:!0}}function dr(e){return e.sample??Ze(e.name)}function Es(e){return e.haplotype!==void 0&&e.sample!==void 0?`${e.sample}#${e.haplotype}`:dr(e)}var Cs=class{constructor(e){this.index=new Map,this.lengths=[],this.onReference=new Uint8Array(0),this.referenceStart=new Float64Array(0),this.referenceEnd=new Float64Array(0);for(let t of e.nodes)this.lengths[this.indexOf(t.id)]=t.length}indexOf(e){let t=this.index.get(e);return t===void 0&&(t=this.lengths.length,this.index.set(e,t),this.lengths.push(0)),t}nodesOf(e){let t=new Int32Array(e.nodeIds.length);return e.nodeIds.forEach((n,o)=>{t[o]=this.indexOf(n)}),t}spanAt(e,t){let n=t>=0&&t<e.length?e[t]:-1;return n>=0&&this.onReference[n]?{start:this.referenceStart[n],end:this.referenceEnd[n]}:void 0}};function Os(e,t){let n=[],o;for(let s of e){o!==void 0&&s.start!==void 0&&s.start>o&&n.push(o-s.start);let r=0;for(let a of s.nodes)n.push(a),r+=t.lengths[a];o=s.start===void 0?void 0:s.start+r}return Float64Array.from(n)}function Bs(e,t,n){let o,s=0,r;for(let a of e){if(a.start===void 0||o!==void 0&&a.start<o)return;o!==void 0&&a.start>o&&s++===n&&(r={start:o,end:a.start});let i=a.start;for(let c of a.nodes){let l=t.lengths[c];s++===n&&(r={start:i,end:i+l}),i+=l}o=i}return r}function _s(e,t,n,o=!0){if(!n||!o)return{ids:e,complete:!0,from:-1,to:-1};let{onReference:s,referenceStart:r,referenceEnd:a}=t,i=-1,c=-1,l=-1/0,u=1/0;for(let h=0;h<e.length;h++){let k=e[h];if(k>=0&&s[k]){let y=a[k],R=r[k];y<=n.start&&y>l&&(l=y,i=h),R>=n.end&&R<u&&(u=R,c=h)}}if(i>=0&&c>=0){let h=e.slice(Math.min(i,c)+1,Math.max(i,c));return{ids:i<c?h:h.reverse(),complete:!0,from:i,to:c}}let p=h=>t.spanAt(e,h),d=i>=0?i:c,m=-1;for(let h=1;d>=0&&m<0&&h<e.length;h++)m=[d-h,d+h].find(k=>p(k)!==void 0)??-1;if(m<0)return{ids:e,complete:!1,from:-1,to:-1};let b=m>d==p(m).start>p(d).start===(d===i),g=b?e.slice(d+1):e.slice(0,d).reverse(),w=g.length>0?g.length-1:-1,S=w<0?p(d):p(b?d+1+w:0),x={contigEnds:S!==void 0,shortBp:S?Math.max(0,n.start-S.end,S.start-n.end):0};return{ids:g,complete:!1,from:d,to:b?e.length:-1,stop:x}}function $e(e,t){return t?e.filter(n=>t.includes(n.sample)).sort((n,o)=>t.indexOf(n.sample)-t.indexOf(o.sample)||n.label.localeCompare(o.label)):e}function ye(e,t,n){let o=e.paths??[],s=y=>O(y.name).name,r=new Set(e.nodes.flatMap(y=>y.stable?.rank===0?[y.stable.refName]:[])),a=o.map(s),i=e.referencePath!==void 0&&a.includes(e.referencePath)?e.referencePath:a.find(y=>r.has(y))??a[0],c=o.filter(y=>s(y)===i).sort((y,R)=>(y.start??0)-(R.start??0)),l=c[0],u=o.filter(y=>!c.includes(y));if(!l||u.length===0)return;let p=new Map;for(let y of u){let R=p.get(y.name);R?R.push(y):p.set(y.name,[y])}let d=new Cs(e),m=l.start??0,f=t&&t.end>t.start?t:void 0,b=c.map(y=>d.nodesOf(y)),g=d.lengths.length;d.onReference=new Uint8Array(g),d.referenceStart=new Float64Array(g),d.referenceEnd=new Float64Array(g);let w=!1,S=!1;for(let[y,R]of c.entries()){let M=R.start??0;for(let I of b[y]){let G=d.lengths[I];d.onReference[I]||(d.onReference[I]=1,d.referenceStart[I]=M,d.referenceEnd[I]=M+G,w||=f!==void 0&&M+G<=f.start,S||=f!==void 0&&M>=f.end),M+=G}}let x=f===void 0||w&&S,h=(y,R)=>{let M=y[0],I=y.map((C,Q)=>({start:C.start,nodes:R?.[Q]??d.nodesOf(C)})).sort((C,Q)=>(C.start??0)-(Q.start??0)),{ids:G,complete:A,from:B,to:F,stop:L}=_s(Os(I,d),d,f,x),v=M.contig??fe(O(M.name).name),N=Bs(I,d,B<0?0:B),_=N?B<0?{contig:v,start:N.start,reversed:!1}:B<F?{contig:v,start:N.end,reversed:!1}:{contig:v,start:N.start,reversed:!0}:void 0,{lengths:$,onReference:H,referenceStart:T,referenceEnd:D}=d,te=[],P,z=0,Z=0,qe=0,ae=0;for(let C of G){if(C<0){P={start:z,bp:-C,onReference:!1,gap:!0},te.push(P),z-=C,qe-=C,ae=0;continue}let Q=$[C],me=H[C]===1,Je=P?.referenceStart,Nt=me&&Je!==void 0&&ae>=0&&Je+P.bp===T[C],as=me&&Je!==void 0&&ae<=0&&D[C]===Je;!me&&P&&!P.onReference&&!P.gap?P.bp+=Q:Nt||as?(P.bp+=Q,Nt||(P.referenceStart=T[C],P.reversed=!0),ae=Nt?1:-1):(P={start:z,bp:Q,onReference:me,referenceStart:me?T[C]:void 0},te.push(P),ae=0),z+=Q,me||(Z+=Q)}return{name:M.name,label:Es(M),sample:dr(M),haplotype:M.haplotype,bp:z,offReferenceBp:Z,gapBp:qe,complete:A,stop:L,runs:te,axis:_}};return{origin:f?f.start:m,unit:n,reference:h(c,b),rows:[...p.values()].map(y=>h(y)).sort((y,R)=>Number(R.complete)-Number(y.complete)||R.bp-y.bp||y.label.localeCompare(R.label))}}var xt=1.3;function ke(e,t={rowPx:U,readouts:!0}){let n=e.reference.bp;for(let o of e.rows)n=Math.max(n,o.bp);return{maxX:e.origin+n*(t.readouts?xt:1),maxY:e.rows.length*t.rowPx}}function xe(e,t,n){return e?n&&!n.labelled?[]:[e.reference,...e.rows].map((o,s)=>({label:o.label,y:s*(n?.rowPx??U)})):t?.rowLabels??[]}function en(e,t){let n=ee(e),o=ye(e,t);if(n.length===0||!o)return;let s=t?n.filter(a=>At(a,t)):n;return{nodePositions:ie(s.length>0?s:n),rowLabels:xe(o),referenceAxis:!0,pixelRows:!0,extent:ke(o)}}var ur="Force-directed layout",Se=e=>e.nodes.some(E),lr=e=>Se(e)&&(e.paths?.length??0)>1,pr=e=>Se(e)&&e.nodes.some(Re),St=[{value:"auto",label:"Anchored",description:"x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.",run:rr,cutMargins:!0,wholeWalks:!1,available:Se,drawsLocally:Se,drawsNodes:!0},{value:"samplerows",label:"Sample rows",description:"x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.",run:Jo,cutMargins:!0,wholeWalks:!1,available:pr,drawsLocally:pr,drawsNodes:!0},{value:"walkrows",label:"Walk rows",description:"x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs a reference and two or more walks.",run:en,cutMargins:!1,wholeWalks:!0,available:lr,drawsLocally:lr,drawsNodes:!1},{value:"ordered",label:"Ordered",description:"x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.",run:cr,cutMargins:!1,wholeWalks:!1,available:Se,drawsLocally:Se,drawsNodes:!0},{value:"tubemap",label:"Tube map",description:"sequenceTubeMap: every path a coloured tube through boxed nodes, columns in node order and node widths log-scaled. Needs P or W lines.",run:nr,cutMargins:!1,wholeWalks:!1,available:_e,drawsLocally:_e,drawsNodes:!1},{value:"tubemapref",label:"Tube map on reference",description:"The tube map with each column at the reference bp it covers, so the tubes line up with the tracks around them. Needs P or W lines and a reference path.",run:or,cutMargins:!0,wholeWalks:!1,available:kt,drawsLocally:kt,drawsNodes:!1},{value:"force",label:ur,description:"OGDF FMMM (wasm) or stress, whichever engine is chosen.",run:()=>{},cutMargins:!1,wholeWalks:!1,available:()=>!0,drawsLocally:()=>!1,drawsNodes:!0}],$s=St.map(e=>e.value);function tn(e,t){return!Y(e).drawsLocally(t)}function Y(e){return St.find(t=>t.value===e)??St[0]}function nn(e){return e.walkStrip&&e.mode.drawsNodes&&!e.drawsPicture&&!e.popped&&!e.host&&e.walks>1}function on(e,t){return e.wholeWalks||t.walkStrip&&!t.host}var We=6,hr=260,Ws=11,Fs=3,Hs="#111",mr=3;function rn(e,t,n){let o=e.pathVisits?.get(n.name)??[],s=[];for(let r of t){let a=r.axis;if(!a)continue;let i=O(r.name).name;for(let c of o){if(c.path!==i)continue;let{start:l,end:u}=qn(a,c.start,c.start+n.length);u>0&&l<r.bp&&s.push({row:r.name,start:l,bp:u-l})}}return s}var fr=new WeakMap;function Ds(e,t){let n=fr.get(e);if(n||(n=new Map,fr.set(e,n)),n.has(t))return n.get(t);let o=new Map(e.nodes.map(i=>[i.id,i.length])),s=O(t).name,r=(e.paths??[]).filter(i=>s===e.referencePath?O(i.name).name===s:i.name===t),a;if(r.every(i=>i.start!==void 0)){a={ids:[],starts:[],ends:[]};for(let i of[...r].sort((c,l)=>c.start-l.start)){let c=i.start;for(let l of i.nodeIds){let u=o.get(l)??0;a.ids.push(l),a.starts.push(c),a.ends.push(c+u),c+=u}}}return n.set(t,a),a}function Xs(e,t,n,o){let s=t.axis,r=s&&Ds(e,t.name);if(!s||!r||n<0||n>t.bp)return;let a=s.reversed?s.start-n:s.start+n,i=.5/o,c=s.reversed?{start:s.start-t.bp,end:s.start}:{start:s.start,end:s.start+t.bp},l=Math.max(a-i,c.start),u=Math.min(a+i,c.end),p=0,d=r.starts.length;for(;p<d;){let g=p+d>>1;r.ends[g]<=l?p=g+1:d=g}let m,f=-1,b=!1;for(let g=p;g<r.starts.length&&r.starts[g]<u;g++){let w=r.ends[g]-r.starts[g],S=r.starts[g]<=a&&a<r.ends[g];(w>f||w===f&&S&&!b)&&(f=w,m=r.ids[g],b=S)}return m}function Fe(e,t){let n=t.maxHeight??hr,o=t.labelPx??Math.max(...[e.reference,...e.rows].map(m=>m.label.length))*be+16,s=e.rows.length+1,{rowPx:r,barPx:a,labelled:i,readouts:c}=it(s,n-2*We,Fs),l=Math.max(e.reference.bp,...e.rows.map(m=>m.bp),1),u=i?o:We,d=Math.max(1,t.width-u-We)/(l*(c?xt:1));return{scaleX:d,scaleY:1,translateX:u-e.origin*d,translateY:We+r/2,width:t.width,height:s*r+2*We,rowPx:r,barPx:a,readouts:c,labelled:i,boxesGenes:at(r,a)}}function Vs(e,t,n,o){let s=Math.round((o-t.translateY)/t.rowPx),r=[e.reference,...e.rows][s],a=(n-t.translateX)/t.scaleX-e.origin;return r&&s>=0&&a>=0&&a<=r.bp?{index:s,row:r,offset:a}:void 0}function js(e,t,n){let o=new Map([e.reference,...e.rows].map((r,a)=>[r.name,a])),s=r=>(e.origin+r)*t.scaleX+t.translateX;return Ie("g",{"data-testid":"graph-walk-marks"},...n.flatMap(r=>{let a=o.get(r.row);if(a===void 0)return[];let i=a*t.rowPx+t.translateY,c=s(r.start),l=Math.max(2,r.bp*t.scaleX),u=p=>Ie("rect",{x:c,y:p,width:l,height:mr,fill:Hs});return[u(i-t.barPx/2-mr-1),u(i+t.barPx/2+1)]}))}function sn(e,t,n=new Set){return Ie("g",{"font-family":"sans-serif","font-size":Ws,fill:"#333"},...(t.labelled?[e.reference,...e.rows]:[]).map((o,s)=>Ie("text",{x:6,y:s*t.rowPx+t.translateY+4,"font-weight":n.has(o.name)?600:void 0},o.label)))}function an(e,t,n){if(t?.size)return e.boxesGenes?n:{untracked:0,unread:0,...n,crowded:!0}}function se(e){return`${e.refName}:${(e.start+1).toLocaleString()}-${e.end.toLocaleString()}`}function Ys(e,t,n=o=>o){return t?{deletion:{bp:`${t.bp.toLocaleString()} bp`,where:se(t)}}:{ends:`${n(e.from)}${e.fromStrand??""} \u2192 ${n(e.to)}${e.toStrand??""}`}}function gr(e){return he(e)?br(e):void 0}function br(e){return{sample:Ze(e.stable.refName),haplotype:Pn(e.stable.refName),refName:fe(e.stable.refName),start:e.stable.start,end:e.stable.start+e.length}}function zs(e,t){let n=[...e].sort((r,a)=>r.start-a.start),o,s;for(let r of n)s=s&&r.start-s.end<=t?{start:s.start,end:Math.max(s.end,r.end)}:{start:r.start,end:r.end},(!o||s.end-s.start>o.end-o.start)&&(o=s);return o}function Us(e){return`${e.haplotype??e.sample}\0${e.refName}`}function wr(e,{maxGap:t=1/0}={}){let n=new Map;for(let s of e.nodes)if(he(s)){let r=br(s),a=Us(r),i=n.get(a);i?(i.spans.push({start:r.start,end:r.end}),i.rank=Math.min(i.rank,s.stable.rank)):n.set(a,{sample:r.sample,haplotype:r.haplotype,refName:r.refName,rank:s.stable.rank,spans:[{start:r.start,end:r.end}]})}let o=new Map;for(let s of n.values()){let r=zs(s.spans,t);if(r){let a={sample:s.sample,haplotype:s.haplotype,refName:s.refName,start:r.start,end:r.end,rank:s.rank,nodeCount:s.spans.length},i=s.haplotype??s.sample,c=o.get(i);(!c||a.nodeCount>c.nodeCount)&&o.set(i,a)}}return[...o.values()].sort((s,r)=>+(s.rank!==0)-+(r.rank!==0)||s.sample.localeCompare(r.sample)||(s.haplotype??"").localeCompare(r.haplotype??""))}function He(e,t){return(t.haplotype===void 0?void 0:e(t.haplotype))??e(t.sample)}function yr(e,t){return e.flatMap(n=>{let o=He(t,n);return o===void 0?[]:[{...n,sample:o}]})}function Rt(e){return`${e.refName}:${e.start+1}-${e.end}`}function K(e){return typeof e=="object"&&e!==null}function Ks(e){return K(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function qs(e){return e.flatMap(t=>K(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function De({views:e,connectedViewId:t,assemblyName:n}){let o=qs(e).filter(r=>Ks(r)).filter(r=>r.assemblyNames.includes(n));return o.find(r=>r.id===t)??(o.length===1?o[0]:void 0)}function cn(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Wc(e,t){let n=e.assemblyManager,o=n?.has(t.assemblyName)?n.get(t.assemblyName):void 0;return o?{...t,assemblyName:o.name,refName:o.getCanonicalRefName2?.(t.refName)??t.refName}:t}function dn(e,t){let n=X(t,"assemblyNames");return Array.isArray(n)?n.filter(o=>typeof o=="string").map(o=>cn(e,o)):[]}function xr(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var Js=1e3;function ln(e,t=Js){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function Sr(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function Fc({session:e,location:t,assembly:n,connectedViewId:o,tracks:s=[]}){let r=De({views:e.views,connectedViewId:o,assemblyName:n}),a;return r?(xr(e,`Could not show ${n} ${se(t)}`,Promise.resolve(r.navToLocString(Rt(t),n))),a=r.id):a=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${se(t)}`,init:{assembly:n,loc:Rt(t),tracks:s}}).id,a}function Hc({session:e,location:t,assembly:n,connectedViewId:o}){De({views:e.views,connectedViewId:o,assemblyName:n})&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n})}function kr(e,t){let n=t===void 0?void 0:e.tracks.find(o=>X(o,"trackId")===t);return n?dn(e,n):[]}function Dc({session:e,contributors:t,trackId:n,graphTrackId:o}){let s=kr(e,o),r=kr(e,n),a=t.filter(l=>r.includes(l.sample)),i=a.length>=2?a:t,c={init:{views:i.map(l=>({assembly:l.sample,loc:Rt(l),...o!==void 0&&s.includes(l.sample)?{tracks:[o]}:{}})),tracks:n?i.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};xr(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c))}function Rr(e){if(typeof e!="object"||e===null)return!1;let t=e;return typeof t.horizontalScroll=="function"&&typeof t.zoomTo=="function"&&"coarseDynamicBlocks"in t&&"dynamicBlocks"in t}function vr(e){return e.reduce((t,n)=>t&&t.end-t.start>=n.end-n.start?t:n,void 0)}function Mr(e,t){let n=vr(e.dynamicBlocks.contentBlocks.filter(r=>r.refName===t.refName&&r.assemblyName===t.assemblyName)),{bpPerPx:o}=e;if(!n||!(o>0))return;let s=n.offsetPx-e.offsetPx;return n.reversed?{scale:-1/o,translateX:s+n.end/o}:{scale:1/o,translateX:s-n.start/o}}function Vc(e){let t=vr(e.dynamicBlocks.contentBlocks),n=t?.displayedRegionIndex===void 0?void 0:e.displayedRegions[t.displayedRegionIndex];return t&&e.bpPerPx>0?{refName:t.refName,assemblyName:t.assemblyName,start:t.start,end:t.end,bpPerPx:e.bpPerPx,span:e.bpPerPx*e.width,regionStart:n?.start??t.start,regionEnd:n?.end??t.end}:void 0}function Zs(e,t,n=!0){let o=e.end-e.start,s=n?Math.max(0,Math.min(e.span,(t-o)/2)):0,r=Math.max(e.regionStart,Math.floor(e.start-s)),a=Math.min(e.regionEnd,Math.ceil(e.end+s)),i=a-r-t;return i>0&&(r+=Math.floor(i/2),a-=Math.ceil(i/2)),{refName:e.refName,assemblyName:e.assemblyName,start:r,end:a}}function jc(e,t,n=!0){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;if(n)return e.start<=t.start+1&&t.end<=e.end+1;let o=Zs(t,1/0,!1);return Math.abs(e.start-o.start)<1&&Math.abs(e.end-o.end)<1}function Xe(e,t,n){let o=new Map;for(let r of e.nodes)if(he(r)){let{refName:a}=r.stable;if(n[r.id]?.length){let i=o.get(a)??o.set(a,{nodes:[],reach:0}).get(a);i.nodes.push(r),i.reach=Math.max(i.reach,r.length)}}for(let{nodes:r}of o.values())r.sort((a,i)=>a.stable.start-i.stable.start);let s=[];for(let r of t){let a=o.get(r.refName);if(!a)continue;let i=[],c=[],l=new Set,u,p=1/0,d=0,m=(r.start+r.end)/2,{nodes:f,reach:b}=a;for(let g=Tt(f,r.start-b);g<f.length&&f[g].stable.start<r.end;g++){let w=f[g],S=w.stable.start,x=S+w.length;if(x<=r.start)continue;let h=n[w.id];l.add(w.id),d+=Math.min(x,r.end)-Math.max(S,r.start);let k=[];for(let M of r.exons){let I=Math.max(M.start,S),G=Math.min(M.end,x);if(G<=I)continue;let A=Ft(h,(I-S)/w.length,(G-S)/w.length);A.length===1&&A.push({...A[0]}),k.push(Le(A))}k.length>0&&(i.push(...k),c.push({nodeId:w.id,d:k.join("")}));let y=Math.min(Math.max(m,S),x),R=Math.abs(y-m);if(R<p){p=R;let M=w.length?(y-S)/w.length:0;u=Ft(h,M,M)[0]}}u&&s.push({gene:r,exons:i.join(""),exonsByNode:c,nodeIds:l,at:u,covered:d/(r.end-r.start)})}return s}var Lr="10.2.7";function Ve(e,t,n={}){return{nodePositions:n.drawsRows?{}:e.nodePositions,deletions:t.bypassed,deletionRoutes:e.deletionRoutes,stranded:e.stranded,hiddenEdges:t.hidden}}var Nr=(e,t)=>!!e.referencePath&&O(t).name===e.referencePath;function Qs(e,t){return(e.paths??[]).filter(n=>n.name===t).sort((n,o)=>(n.start??0)-(o.start??0))}function Pr(e,t){let n=Qs(e,t),o=n[0];if(!o)return;let s=new Map(e.nodes.map(x=>[x.id,x])),r=new Map;e.edges.forEach((x,h)=>{r.set(`${x.from}>${x.to}`,h)});let a=x=>s.get(x)?.length??0,i=x=>x.nodeIds.reduce((h,k)=>h+a(k),0),c=n.reduce((x,h)=>x+i(h),0),l=x=>{let h=Math.min(...x.map(k=>k.start??1/0));return Number.isFinite(h)?{start:h,end:Math.max(...x.map(k=>(k.start??0)+i(k)))}:void 0},u=l(n),p=u&&{contig:o.contig??fe(O(t).name),...u},d=p?p.end-p.start:c,m=new Set,f=new Set,b=new Map,g=0;for(let x of n)p&&(g=Math.max(g,(x.start??0)-p.start)),x.nodeIds.forEach((h,k)=>{if(m.add(h),k>0){let R=x.nodeIds[k-1],M=r.get(`${R}>${h}`)??r.get(`${h}>${R}`);M!==void 0&&f.add(M)}let y=a(h);b.has(h)||b.set(h,d>0?(g+y/2)/d:0),g+=y});let w=Nr(e,t),S=()=>{let x=w?[]:(e.paths??[]).filter(k=>Nr(e,k.name));if(x.length===0)return;let h=l(x);return h?h.end-h.start:x.reduce((k,y)=>k+i(y),0)};return{name:t,reference:w,range:p,nodeIds:m,edgeIndexes:f,progress:b,steps:n.reduce((x,h)=>x+h.nodeIds.length,0),bp:c,referenceBp:S()}}function Ar(e,t,n,o){let s=new Map(e.nodes.map(a=>[a.id,a])),r=new Map;for(let[a,i]of t.progress){let c=s.get(a),l=o?.midpoints.get(a),u=n.field==="progress"?i:o&&l!==void 0&&!(c?.stable&&c.stable.rank>0)?(l-o.start)/o.span:void 0;r.set(a,to(n,u))}return r}function ea(e,t){let n=new Set,o=0,s=e.referencePath;if(!s||t.reference)return{reversed:n,bp:o};let r=e.pathVisits;if(!r)return{reversed:n,bp:o};let a=r.pathIndex(O(t.name).name),i=r.pathIndex(s),c=new Map(e.nodes.map(l=>[l.id,l]));for(let l of t.progress.keys()){let u=c.get(l),p=u?r.slot(u.name):-1,d=p<0?-1:r.firstBy(p,a),m=p<0?-1:r.firstBy(p,i);d>=0&&m>=0&&r.reversed[d]!==r.reversed[m]&&(n.add(l),o+=u.length)}return{reversed:n,bp:o}}function je(e,t,n){let o=new Set,s=t.filter(i=>!o.has(i.walk)&&o.add(i.walk)).flatMap(i=>{let c=Pr(e,i.walk);return c?[{walk:c,layer:i}]:[]}).sort((i,c)=>Number(c.walk.reference)-Number(i.walk.reference));if(s.length===0)return;let r=0,a=s.map(({walk:i,layer:c})=>{let l=Yt(c,i.reference,i.reference?0:r++,s.length===1),{reversed:u,bp:p}=ea(e,i);return{...i,encoding:l,colors:Ar(e,i,l,n),reversed:u,reversedBp:p}});return Tr(a,n)}var ta={field:"progress",scheme:"red"};function Ye(e,t,n,o){return t.walks.map(s=>{let r=n.find(i=>i.walk===s.name)?.color,a=Yt({walk:s.name,color:{...ta,...r}},s.reference,0);return Tr([{...s,encoding:a,colors:Ar(e,s,a,o)}],o)})}function Tr(e,t){return{walks:e,referenceDomain:t?{start:t.start,end:t.start+t.span}:void 0,nodeIds:new Set(e.flatMap(n=>[...n.nodeIds])),edgeIndexes:new Set(e.flatMap(n=>[...n.edgeIndexes])),names:new Set(e.map(n=>n.name))}}var ue={...jt,colorScheme:"auto",nodeWidth:"depth",contigThickness:6,connectorThickness:2};function pn(e){let t=ue,n={};for(let[o,s]of Object.entries(e))s!==void 0&&s!==t[o]&&(n[o]=s);return n}var Gr=[{value:"auto",label:"Auto"},{value:"uniform",label:"Uniform"},{value:"random",label:"Random"},{value:"rainbow",label:"Rainbow"},{value:"depth",label:"Depth"},{value:"node-length",label:"Node length"},{value:"stable-rank",label:"Stable rank"},{value:"reference-position",label:"Reference position"},{value:"grey",label:"Grey"}],na=Gr.map(e=>e.value);function ze(e,t){return e!=="auto"?e:t?.anchoredBy?"reference-position":"uniform"}function Ir(e,t,n){let o=n.region,s=n.colorDomain??o,r=n.walkRows,a=Oe(t,{region:n.fitToDrawing?void 0:o,extent:r&&t.extent?ke(r,n.walkRowPitch):void 0}),i=new Map(e.nodes.map(h=>[h.id,h])),c=ze(n.colorScheme??ue.colorScheme,e),l=c==="reference-position"&&!t.tubeMap?Ge(e,s):void 0,u=Pe(e,t.tubeMap?[]:Ne(e),n.showDeletionEdges),p=n.walks??[],d=p.some(h=>h.color?.field==="reference")?l??Ge(e,s):void 0,m=p.length>0&&!t.tubeMap?je(e,p,d):void 0,f=lt(n.facet),b=f.field&&m&&m.walks.length>1?Ye(e,m,p,d):void 0,g=nt(e.paths?.length?Ae(e.paths):[]),w=n.referenceName??Et(e,o),S=n.contigThickness??ue.contigThickness,x=n.nodeWidth??ue.nodeWidth;return{bounds:a,nodeById:i,colorScheme:c,referenceRamp:l,drawnDeletions:u,layers:p,lift:m,facet:f,panels:b,labelOf:h=>g.get(h)??h,referenceName:w,reference:m?.referenceDomain&&{...m.referenceDomain,name:w},contigThickness:S,nodeWidth:x,geometry:(h,k)=>st({...Ve(t,u,{drawsRows:!!r}),graph:e,nodeById:i,colorScheme:c,contigThickness:S,connectorThickness:n.connectorThickness??ue.connectorThickness,drawPaths:!1,nodeWidth:x,linearLayout:n.linearLayout,highlight:h,axis:k,referenceRamp:l})}}var mn='font-family="Helvetica, Arial, sans-serif" font-size="11"',oa=48,vt=18,ra=16,sa=22,aa="rgb(160,160,160)",Cr="#1c1c22";function un(e,t,n,o,s,r,a,i=1){let c=o.length>1?oa:vt,l=o.length>1?`fill="url(#${e})"`:`fill="${o[0].color}"${i<1?` fill-opacity="${i}"`:""}`,u=o.length>1?`<linearGradient id="${e}">${o.map(d=>`<stop offset="${d.offset}" stop-color="${d.color}"/>`).join("")}</linearGradient>`:"";return{width:Math.max(c+5+(s.length+r.length)*be,(a?.length??0)*be),markup:`${u}<g transform="translate(${t} ${n})" ${mn}><rect y="5" width="${c}" height="8" rx="2" ${l}/><text x="${c+5}" y="13"><tspan font-weight="bold">${ne(s)}</tspan>${ne(r)}</text>${a?`<text y="28">${ne(a)}</text>`:""}</g>`}}function ia(e,t){return{width:vt+5+4*be,markup:`<g transform="translate(${e} ${t})" ${mn}><rect x="1" y="4" width="${vt-2}" height="10" rx="4" fill="none" stroke="${qt}" stroke-width="2"/><text x="${vt+5}" y="13">exon</text></g>`}}function Er(e,t,n,o,s,r){let a=Oo(o,r);return un(e,t,n,zt(o.encoding),s,a.delta+a.outside+a.reversed,a.scale)}function ca(e,t){return e.replaceAll(/([ML])(-?[\d.e-]+),(-?[\d.e-]+)/g,(n,o,s,r)=>`${o}${+(Number(s)*t.scaleX+t.translateX).toFixed(1)},${+(Number(r)*t.scaleY+t.translateY).toFixed(1)}`)}function da(e,t,n,o,s){return`<rect x="${e-n/2}" y="${t-Me-Wt+2}" width="${n}" height="${Me+Wt*2-2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${qt}"/><text x="${e}" y="${t}" font-family="Helvetica, Arial, sans-serif" font-size="${Me}" fill="${Cr}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${ne(o)}</tspan>${s?ne(s):""}</text>`}function fn(e,t,n={}){let o=n.width??1200,s=n.height??800,r=n.walkRows,{bounds:a,nodeById:i,referenceRamp:c,layers:l,lift:u,facet:p,panels:d,labelOf:m,referenceName:f,reference:b,contigThickness:g,nodeWidth:w,geometry:S}=Ir(e,t,n),x=t.pixelRows??!1,h=c&&{start:c.start,end:c.start+c.span},k=n.genes?.length&&!t.tubeMap&&!r?Xe(e,n.genes,t.nodePositions):[],y=ot(e,i,g,w),R=0;function M(L,v,N,_){let $=[],H=To(Ao(k,y.halfWidthPx,L,P=>ca(P,v)),{id:`exons${R++}`,width:N,height:_});H&&$.push(de(H));let T=P=>({x:P.x*v.scaleX+v.translateX,y:P.y*v.scaleY+v.translateY}),D={width:N,height:_};for(let{item:P,x:z,y:Z,w:qe,text:ae}of Wn(Io(k,T,g,Go(t.nodePositions,v)),D,$n(D))){let C=T(P.at).y+g/2;$.push(`<line x1="${z}" x2="${z}" y1="${Z-Me-2}" y2="${C}" stroke="${Cr}" stroke-width="0.8" stroke-opacity="0.6"/>`,da(z,Z,qe,P.gene.name,ae.slice(P.gene.name.length)))}r&&$.push(de(Vt(r,{...v,width:N,height:_,...n.walkRowPitch},{ramp:h,rowGenes:n.rowGenes})));let te=xe(r,t,n.walkRowPitch);for(let{label:P,y:z}of te){let Z=z*v.scaleY+v.translateY;Z>=0&&Z<=_&&$.push(`<text x="6" y="${Z+4}" ${mn} stroke="#fff" stroke-width="3" paint-order="stroke">${ne(P)}</text>`)}return $.join("")}function I(L,v,N){let _=Ce(a,v,N,x,d?{padLeft:J,padTop:J,padRight:J,padBottom:J}:{});if(!_)return"";let $=ut(_.scale,x),{canvas:H,markup:T}=No(v,N),D=new Po(H);D.uploadGeometry(S(L,$));let te={scaleX:$.scaleX,scaleY:$.scaleY,translateX:_.translateX,translateY:_.translateY};return D.updateTransform({...te,dpr:1}),D.render([1,1,1,1]),T()+M(L,te,v,N)}let G=[],A;if(d){let L=pt(d.map(N=>N.walks[0].name),p.field||"walk",p.domain),v=dt({count:L.count,bounds:a,pixelRows:x,width:o,room:s,columns:L.columns??p.columns});d.forEach((N,_)=>{let $=L.cells[_],H=$%v.columns*(v.width+Ee),T=Math.floor($/v.columns)*(v.height+ct+Ee),D=N.walks[0];G.push(Er(`key${_}`,H+6,T+2,D,m(D.name),b).markup,`<svg x="${H}" y="${T+ct}" width="${v.width}" height="${v.height}">${I(N,v.width,v.height)}</svg>`)}),A=v.total}else{let L=6,v=T=>{G.push(T.markup),L+=T.width+ra};if(u&&(u.walks.forEach((T,D)=>{v(Er(`key${D}`,L,2,T,m(T.name),b))}),v(un("faded",L,2,[{offset:0,color:aa}],"",`not on ${u.walks.length===1?m(u.walks[0].name):"these walks"}`,void 0,.3))),r){let T=Xt(Dt(r,{ramp:h,genes:n.rowGenes?.size?n.rowGeneGaps:void 0}),L,2,"rows-key");v({width:T.width,markup:de(T.tree)})}else!u&&c&&v(un("ramp",L,2,zt({field:"reference",scheme:"rainbow"}),f?`${f} position`:"Reference position","",Co(f,c.start,c.start+c.span)));k.some(T=>T.exonsByNode.length>0)&&v(ia(L,2));let N=G.length>0?ct:0,_=o-2*W,$=x||!(a.w>0)?a.h:a.h*_/a.w,H=Math.max(160,Math.min(s-N,Math.ceil($+2*W)));G.push(`<svg y="${N}" width="${o}" height="${H}">${I(u,o,H)}</svg>`),A=N+H}let B=n.walkStrip;if(B&&!r&&!t.tubeMap){let L=Fe(B.rows,{width:o}),v=Xt(Dt(B.rows,{ramp:h,genes:an(L,B.rowGenes,B.rowGeneGaps)}),6,A+L.height,"strip-key");G.push(`<line x1="0" x2="${o}" y1="${A+.5}" y2="${A+.5}" stroke="#ddd"/>`,`<svg y="${A}" width="${o}" height="${L.height}">${de(Vt(B.rows,L,{ramp:h,rowGenes:B.rowGenes,idPrefix:"strip"}))}${de(sn(B.rows,L,new Set(l.map(N=>N.walk))))}</svg>`,de(v.tree)),A+=L.height+sa}let F=JSON.stringify({generator:`@jbrowse/bandage-core@${Lr}`,...n.spec===void 0?{}:{spec:n.spec}});return`<svg xmlns="http://www.w3.org/2000/svg" width="${o}" height="${A}" viewBox="0 0 ${o} ${A}"><metadata>${ne(F)}</metadata><rect width="${o}" height="${A}" fill="#fff"/>${G.join("")}</svg>
+`}var Or=.9;function Ue(e,t){return e+2>=t||e>=Or*t}var Br=50;function hn(e,t,n,o=[]){let s=new Map(e.nodes.map(a=>[a.name,a])),r=[];for(let a of t){let i=[],c=1/0,l=-1/0,u=1/0,p=[],d=le(a);for(let[b,g]of d.entries()){let w=s.get(g),S=w&&n[w.id];if(!(!w||!S?.length)&&!(a.key?b===0||b===d.length-1:E(w)&&(w.stable.start<a.start||w.stable.start>=a.end))){p.push(w.id),i.push(Le(S.length===1?[S[0],S[0]]:S));for(let x of S)c=Math.min(c,x.x),l=Math.max(l,x.x),u=Math.min(u,x.y)}}if(p.length===0)continue;let m={x:(c+l)/2,y:u},f=a.covering===!0||Ue(p.length,e.nodes.length);r.push({bubble:a,...fo(a,o),path:i.join(""),labelAt:m,members:p.length,nodeIds:p,whole:f,tick:!f&&!a.partial&&a.longestAlleleLength<Br})}return r}function Ke(e,t){let n=new Set(t),o=e.nodes.filter(c=>n.has(c.name)),s=new Set(o.map(c=>c.id)),r=new Map(e.nodes.map(c=>[c.id,c.length])),a=new Map,i=e.paths?.flatMap(c=>{let l=c.nodeIds.findIndex(d=>s.has(d));if(l<0)return[];let u=c.nodeIds.filter(d=>s.has(d));a.set(c.name,{first:l,nodeIds:u});let p=c.nodeIds.slice(0,l).reduce((d,m)=>d+(r.get(m)??0),0);return[{...c,nodeIds:u,...c.start===void 0?{}:{start:c.start+p}}]});return{name:e.name,nodes:o,edges:e.edges.filter(c=>s.has(c.from)&&s.has(c.to)),...i?.length?{paths:i}:{},anchorPaths:_n(e,a),pathVisits:e.pathVisits,anchoredBy:e.anchoredBy,referencePath:e.referencePath}}function gn(e,t,n,o){let s=e.get(t);e.set(t,{min:Math.min(s?.min??1/0,n.min+o),max:Math.max(s?.max??-1/0,n.max+o),n:Math.min(mo,n.n+(s?.n??0))})}function _r(e){if(!e.nodes.some(E))return[];let t=new Map(e.nodes.map(d=>[d.id,d])),n=Qt(e),o=new Map(n.map((d,m)=>[d,m])),s=new Int32Array(n.length+1),r=new Map,a=new Set;for(let d of e.edges){let m=o.get(d.from),f=o.get(d.to);if(m===void 0||f===void 0||m===f)continue;a.add(`${d.from}>${d.to}`).add(`${d.to}>${d.from}`);let[b,g]=m<f?[m,f]:[f,m];s[b+1]++,s[g]--;let[w,S]=m<f?[d.from,d.to]:[d.to,d.from];(r.get(w)??r.set(w,new Set).get(w)).add(S)}for(let d=1;d<s.length;d++)s[d]+=s[d-1];let i=e.nodes.filter(E).sort((d,m)=>d.stable.start-m.stable.start),c=new Set([i[0].id,i.at(-1).id]),l=i.map(d=>[d,o.get(d.id)]).filter(([d,m])=>c.has(d.id)||s[m]===0).sort(([d,m],[f,b])=>m-b||d.stable.start-f.stable.start),u=bn(e,l.map(([d])=>d.id)),p=[];for(let d=0;d+1<l.length;d++){let[m,f]=l[d],[b,g]=l[d+1],w=n.slice(f+1,g);if(w.length===0)continue;let S=new Map([[m.id,{min:0,max:0,n:1}]]);for(let F of[m.id,...w]){let L=S.get(F);if(L)for(let v of r.get(F)??[])o.get(v)>g||gn(S,v,L,v===b.id?0:t.get(v).length)}let x=u&&wn(e,t,u,m.id,b.id),h=x?.n?x:void 0,k=h??S.get(b.id)??{min:0,max:0,n:0},y=x!==void 0&&x.left>0,R=m.stable.start+m.length,M=b.stable.start,I=[m.id,...w.filter(F=>E(t.get(F))),b.id],G=I.some((F,L)=>L>0&&!a.has(`${I[L-1]}>${F}`)),A=G||y,B=G&&!h;p.push({refName:m.stable.refName,start:R,end:M,segmentCount:w.length+2,pathCount:k.n,inversion:!1,shortestAlleleLength:B?M-R:k.min,longestAlleleLength:B?M-R:k.max,segments:[m,...w.map(F=>t.get(F)),b].map(F=>F.name).join(","),shortestAllele:void 0,longestAllele:void 0,partial:A,routes:h?.routes})}return p}function bn(e,t){let n=e.paths;if(!n)return;let o=new Map;for(let s of t)o.set(s,new Int32Array(n.length).fill(-1));return n.forEach((s,r)=>{let a=s.nodeIds;for(let i=0;i<a.length;i++){let c=o.get(a[i]);c?.[r]===-1&&(c[r]=i)}}),o}function wn(e,t,n,o,s){let r=[],a=1/0,i=-1/0,c=0,l=n.get(o),u=n.get(s);return e.paths.forEach((p,d)=>{let m=l[d],f=u[d];if(m<0||f<0){(m>=0||f>=0)&&c++;return}let b=p.nodeIds,g=Math.min(m,f)+1,w=Math.max(m,f),S=f<m?h=>b[w-1-h]:h=>b[g+h],x=r.find(h=>h.steps.length===w-g&&h.steps.every((k,y)=>k===S(y)));if(!x){let h=Array.from({length:w-g},(y,R)=>S(R)),k=0;for(let y of h)k+=t.get(y)?.length??0;x={steps:h,bp:k,walks:[]},r.push(x)}x.walks.push(p.name),a=Math.min(a,x.bp),i=Math.max(i,x.bp)}),r.length||c?{min:a,max:i,n:r.length,left:c,routes:r}:void 0}function la(e,t){let n=e.nodes.length*2,o=new Set,s=[],r=new Int32Array(n);for(let l of e.edges){let u=t.get(l.from),p=t.get(l.to);if(u===void 0||p===void 0)continue;let d=ce(l),m=u*2+(d.from==="end"?1:0),f=p*2+(d.to==="end"?1:0),b=Math.min(m,f)*n+Math.max(m,f);o.has(b)||(o.add(b),s.push(m,f),r[m]++,m!==f&&r[f]++)}let a=new Int32Array(n+1);for(let l=0;l<n;l++)a[l+1]=a[l]+r[l];let i=new Int32Array(a[n]),c=a.slice(0,n);for(let l=0;l<s.length;l+=2){let u=s[l],p=s[l+1];i[c[u]++]=p,u!==p&&(i[c[p]++]=u)}return{offset:a,next:i}}function pa(e,t,n){let o=new Int32Array(e),s=new Uint8Array(e*2),r=new Int32Array(e*2),a=new Int32Array(e),i=[],c=0;return l=>{let u=l>>1;c++,i.length=0;let p=0,d=0,m=0,f,b=g=>{s[g]||(s[g]=1,p++,i.push(g))};b(l),r[d++]=l;e:for(;d>0;){let g=r[--d],w=g>>1;if(o[w]=c,w!==u&&(a[m++]=g),s[g]&&(s[g]=0,p--),t[g]===t[g+1])break;for(let S=t[g];S<t[g+1];S++){let x=n[S],h=x>>1;if(h===u)break e;if(b(x^1),o[h]===c)continue;let k=!0;for(let y=t[x];y<t[x+1];y++)if(o[n[y]>>1]!==c){k=!1;break}k&&(r[d++]=x^1)}if(d===1&&p===1){m>0&&(f={source:l,sink:r[0],inside:a.slice(0,m)});break}}for(let g of i)s[g]=0;return f}}function ua(e){return{source:e.sink^1,sink:e.source^1,inside:e.inside.map(t=>t^1).reverse()}}var Fr=new Intl.Collator(void 0,{numeric:!0});function yn(e,t){return E(e)&&E(t)&&e.stable.refName===t.stable.refName}function $r(e,t){let n=t[e.source>>1],o=t[e.sink>>1],s=yn(n,o)?n.stable.start-o.stable.start:0,r=((e.sink^1)&1)-(e.source&1);return(s||r||Fr.compare(n.name,o.name))<0}function Wr(e){return[e.source>>1,...Array.from(e.inside,t=>t>>1),e.sink>>1]}function ma(e){let{nodes:t}=e,n=new Map(t.map((c,l)=>[c.id,l])),{offset:o,next:s}=la(e,n),r=pa(t.length,o,s),a=new Map;for(let c=0;c<t.length*2;c++){let l=r(c);if(!l)continue;let u=l.source>>1,p=l.sink>>1,d=Math.min(u,p)*t.length+Math.max(u,p);($r(l,t)||!a.has(d))&&a.set(d,l)}return{found:[...a.values()].map(c=>$r(c,t)?c:ua(c)),offset:o,next:s}}function fa(e,t,n,o){let s=o.sink>>1,r=new Map([[o.source>>1,{min:0,max:0,n:1}]]);for(let a of[o.source,...o.inside]){let i=r.get(a>>1);if(i)for(let c=t[a];c<t[a+1];c++){let l=n[c]>>1;gn(r,l,i,l===s?0:e[l].length)}}return r.get(s)??{min:0,max:0,n:0}}function kn(e,t){let{nodes:n}=e,{found:o,offset:s,next:r}=ma(e),a=o.map(f=>Ue(f.inside.length,n.length)),i=o.map(Wr),c=new Map;i.forEach((f,b)=>{for(let g of f)(c.get(g)??c.set(g,[]).get(g)).push(b)});let l=(f,b)=>c.get(f.inside[0]>>1).some(g=>g!==b&&!a[g]&&i[g].length>i[b].length&&i[b].every(w=>c.get(w).includes(g))),u=f=>t!==void 0||yn(n[f.source>>1],n[f.sink>>1]),p=o.filter((f,b)=>!a[b]&&u(f)&&!l(f,b)),d=new Map(n.map(f=>[f.id,f])),m=bn(e,p.flatMap(f=>[n[f.source>>1].id,n[f.sink>>1].id]));return p.map(f=>{let b=n[f.source>>1],g=n[f.sink>>1],w=m&&wn(e,d,m,b.id,g.id),S=w?.n?w:void 0,x=S??fa(n,s,r,f),h=yn(b,g);return{refName:h?b.stable.refName:t.refName,start:h?b.stable.start+b.length:t.start,end:h?g.stable.start:t.end,segmentCount:f.inside.length+2,pathCount:x.n,inversion:!1,shortestAlleleLength:x.min,longestAlleleLength:x.max,segments:Wr(f).map(k=>n[k].name).join(","),shortestAllele:void 0,longestAllele:void 0,partial:w!==void 0&&w.left>0,routes:S?.routes,key:`${b.name}>${g.name}`,...h?{}:{offReference:!0}}}).sort((f,b)=>f.start-b.start||f.end-b.end||Fr.compare(f.key,b.key))}function Mt(e,t){let n=e.nodes.length,o=_r(e);if(o.length===0){let s=kn(e,t);return t?[...s,{...t,covering:!0}]:s}return o.flatMap(s=>Ue(s.segmentCount-2,n)?[...kn(s.segmentCount===n?e:Ke(e,le(s)),s),{...s,covering:!0}]:[s])}function xn(e,t,n){if(t==="uniform"||t==="grey")return;let o={...zn(e),referenceRamp:n};return new Map(e.nodes.map((s,r)=>[s.id,jn(Un(s,r,t,o))]))}var Lt=JBrowseExports["@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"];var Hr=Lt&&Lt.__esModule?Lt.default:Lt;var Sn={paths:!1,bubbles:!1,deletions:!0,genes:!0,referenceStrip:!0,walkStrip:!1};function Dr(e){let t=K(e)?e:{};return new Set(Object.keys(Sn).filter(n=>t[n]??Sn[n]))}function ff(e,t,n){let{[t]:o,...s}=K(e)?e:{};return n===Sn[t]?s:{...s,[t]:n}}var Rn={depth:"depth",length:"node-length",rank:"stable-rank",position:"reference-position"},Xr=Object.fromEntries(Object.entries(Rn).map(([e,t])=>[t,e]));function Vr(e){if(e==="grey"||e==="uniform")return e;if(K(e)){let{field:t,scheme:n}=e;if(t==="id")return n==="rainbow"?"rainbow":"random";if(typeof t=="string"&&t in Rn)return Rn[t]}return"auto"}function jr(e){return K(e)&&typeof e.domainMin=="number"&&typeof e.domainMax=="number"?{start:e.domainMin,end:e.domainMax}:void 0}function bf(e,t){return e==="grey"||e==="uniform"?e:e==="random"?{field:"id",scale:"categorical"}:e==="rainbow"?{field:"id",scheme:"rainbow"}:e==="reference-position"&&t?{field:"position",domainMin:t.start,domainMax:t.end}:Xr[e]?{field:Xr[e]}:{}}var Yr=6;function vn(e){return typeof e=="number"?{width:"uniform",px:e}:K(e)?{width:e.field==="depth"?"depth":"uniform",px:typeof e.value=="number"?e.value:Yr}:{width:"depth",px:Yr}}function kf(e,t){return e==="depth"?{field:"depth",value:t}:t}function ha(e,t,n){let o=Gn(e,t);return o?Bt(o,n):void 0}function zr(e){try{return e()}catch{return}}function Ur(e){let t=new Map;for(let n of e.nodes)t.set(n.id,n);return t}function Kr(e,t,n){return t&&n?$t({nodeId:e,nodeById:t,neighbors:n}):void 0}var qr=uo.views(e=>({sessionTrack(t){return q(e).tracks.find(n=>n.trackId===t)},get grammar(){return{}},get hasPendingSource(){return!1},get canRetryLoad(){return!1},get sourceTrack(){return zr(()=>Ln(e).configuration)},get containingView(){return zr(()=>Pt(e))}})).views(e=>{let t=r=>In(r,{equals:(a,i)=>JSON.stringify(a)===JSON.stringify(i)}),n=t(()=>jr(e.grammar.color)),o=t(()=>lt(e.grammar.facet)),s=t(()=>{let r=ko(e.grammar.facet);return r&&r.field!=="walk"&&r.field!=="sample"?r:void 0});return{get chosenLayoutMode(){return e.grammar.layoutMode??"force"},get chosenColorScheme(){return Vr(e.grammar.color)},get statedColorDomain(){return n.get()},get chosenHover(){return e.grammar.hover??"nodes"},get nodeWidth(){return vn(e.grammar.size).width},get contigThickness(){return vn(e.grammar.size).px},get layerSet(){return Dr(e.grammar.layers)},get drawPaths(){return this.layerSet.has("paths")},get showBubbles(){return this.layerSet.has("bubbles")},get showDeletionEdges(){return this.layerSet.has("deletions")},get showGenes(){return this.layerSet.has("genes")},get showReferenceStrip(){return this.layerSet.has("referenceStrip")},get walkStrip(){return this.layerSet.has("walkStrip")},get facetSetting(){return o.get()},get walkRowGroupBy(){return s.get()},get walkRowSamples(){let r=e.grammar.rows?.kept;return Array.isArray(r)?r:void 0},get hoverLightsEverything(){return this.chosenHover==="everything"},get litNode(){return this.chosenHover==="off"?null:e.hoveredNode}}}).views(e=>({get paneWidth(){return Pt(e).width},get paneMeasured(){return!0},get drawnGraph(){return e.layoutResult?.tubeMap?.graph??e.graph}})).views(e=>({get nodeById(){return e.drawnGraph&&Ur(e.drawnGraph)},get nodeLengths(){let t=new Map;for(let n of e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get legendAtRest(){return e.hoveredNode===null&&e.hoveredRowWalks.length===0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return lo(e)},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!this.geometryPainted)},get canCancelLoad(){return 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!ao.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===no)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 Set(t.map(ht));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(ht(o))&&n.add(ht(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Hn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?qo(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?X(t,"trackId"):void 0},get sessionTracks(){let t=q(e);return t.tracks.map(n=>({trackId:n.trackId,name:X(n,"name"),adapterType:X(n,"adapter").type,assemblies:dn(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&cn(q(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>bt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Vo.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return jo(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return wt(e.geneTrackChoices,e.geneTrackId)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?It(e.graph):void 0},get cutWalkRows(){let t=e.walkCut?.walkRowRuns;return t?Bt(t):e.graph?ye(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=q(e),o=n.has(t)?n.get(t):void 0,s=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(a=>s[a]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t=e.containingView;if(!t)return;let n=Yo(t,e.geneTrack?.trackId);return n.length?new Hr({filters:n,jexl:Nn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?zo(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?ha(n,t,t.unit):ye(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[s,...r]=Uo([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 yo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Lo(t,n),s=(e.graph?.paths??[]).map(r=>O(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:vo(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 t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?xo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Be(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?Xe(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){Be(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:hn(e.graph,e.bubbles,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return ut(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get 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?Mo(o,t.referencePath,r.valueOf,r.palette):s==="tinted"?Kt(o,t.referencePath,Ro):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 Kr(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&&Ur(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?Kr(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 Jr=qr.views(e=>({get host(){let t=e.containingView;return Rr(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 t?wr(t,{maxGap:n.length>0?Gt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=q(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,a])=>[a,r])),s=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>s(o.get(r))??s(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(bt.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let s=wt(o,"");return s?[[n,s]]:[]}))}})).views(e=>({get launchableAssemblies(){return yr(Sr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&De({views:[...q(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?gr(n):void 0,s=o?He(e.assemblyResolver,o):void 0,r=e.graphRegion,a=r?e.nodeSpan(t):void 0,i=r&&a?{sample:r.assemblyName,haplotype:void 0,refName:r.refName,...a}:void 0;return{own:o&&s?{location:ln(o),assembly:s}:void 0,reference:r&&i?{location:ln(i),assembly:r.assemblyName}:void 0,highlight:r&&i?{location:i,assembly:r.assemblyName}:void 0}}}));var Zr=Jr.views(e=>({get walkStripShown(){return nn({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:$e(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Fe(t,{width:e.paneWidth})},get cutsWholeWalks(){return on(Y(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?rn(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:He(e.assemblyResolver,o),span:{refName:n.contig,...Jn(n,t.bp)}}},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:gt(e.nodePositions?.[t],e.toScreen)}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,s=0;for(let r of t.rows){if(!r.axis){s++;continue}let{assembly:a,span:i}=e.rowLocation(r,r.axis),c=a?e.geneTracksByAssembly.get(a):void 0;if(!a||!c){o++;continue}n.push({row:r.name,trackId:c.trackId,region:{assemblyName:a,...i}})}return{reads:n.slice(0,Ut),gaps:{untracked:o,unplaced:s,unread:Math.max(0,n.length-Ut)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let{sample:s,haplotype:r,assembly:a,span:i}=e.rowLocation(o,o.axis);return{label:o.label,assembly:t===0?e.graphRegion?.assemblyName:a,location:{sample:s,haplotype:r,...i}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?Zn([t.reference,...t.rows],n):void 0}}));var Qr=Zr.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&Y(e.drawnLayoutMode??e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostBpFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?Mr(t,n):void 0}})).views(e=>({get hostFrame(){return e.hostPlacesX?e.hostBpFrame:void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?bo(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t?ho(t):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap;return t?.coarse?go(t,t.coarse.deviations):[]},get tubeMapConnectedBoxes(){let t=this.tubeMapReference,{layoutResult:n}=e;return t&&!n?.referenceAxis&&!n?.tubeMapPanels?[...t.values()].flat():void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes&&!e.layoutResult?.tubeMapPanels?_o(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;if(!e.showReferenceStrip||!e.referenceStripApplies||!t)return[];let n=Ho(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}),o=e.walkLift?void 0:e.openBubbleFocus;return o?n.map(s=>o.nodeIds.has(s.node)?s:{...s,colors:[rt],faded:!0}):n}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.hostBpFrame!==void 0},get referenceStripOverhangs(){let t=e.hostBpFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:o}=Do(e.referenceStripBlocks,t,e.paneWidth);return n>0||o>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=e.hoveredNode===null?e.hoveredBubble:null;if(t&&!t.offReference){let s=e.bubbleHalos.find(r=>ft(r.bubble,t));return{start:t.start,end:t.end,anchor:s?e.toScreen(s.labelAt):void 0}}let n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeSpan(n);return o&&n!==null?{...o,anchor:gt(e.nodePositions?.[n],e.toScreen)}:void 0},referenceStripNodeAt(t,n){let o=e.hostBpFrame;return e.referenceStripShown&&o?Xo(e.referenceStripBlocks,o,t,n):void 0},get referenceStripZonePx(){return e.referenceStripShown?Fo:0}}));var ga=3e3,ba=350,wa=34;function ya(e){let t=[0];for(let n=1;n<e.length;n++)t.push(t[n-1]+Math.hypot(e[n].x-e[n-1].x,e[n].y-e[n-1].y));return t}function ka(e,t){if(e.length===1||t===1)return Array.from({length:t},()=>({...e[0]}));let n=ya(e),o=n.at(-1),s=[],r=1;for(let a=0;a<t;a++){let i=o*a/(t-1);for(;r<e.length-1&&n[r]<i;)r++;let c=n[r]-n[r-1],l=c>0?(i-n[r-1])/c:0,u=e[r-1],p=e[r];s.push({x:u.x+(p.x-u.x)*l,y:u.y+(p.y-u.y)*l})}return s}var xa=400,es=1.8,Sa=.1;function ng(e,t,n,o,s){let r=h=>({x:(h.x*t.scaleX+t.translateX-o.translateX)/o.scaleX,y:(h.y*t.scaleY+t.translateY-o.translateY)/o.scaleY}),a={};for(let[h,k]of Object.entries(n)){let y=e[h];y?.length&&k.length&&(a[h]=ka(y.map(r),k.length))}let i=new Map,c=(h,k)=>{let y=i.get(h);y?y.push(k):i.set(h,[k])};for(let h of s){let{from:k,to:y}=h;if(k!==y&&n[k]?.length&&n[y]?.length){let R=ce(h);c(k,{id:y,side:R.to}),c(y,{id:k,side:R.from})}}let l=new Map,u=h=>l.get(h.id)??(h.side==="start"?a[h.id][0]:a[h.id].at(-1)),p=Object.keys(a),d=[];for(let h of p)for(let k of i.get(h)??[]){if(a[k.id]||l.has(k.id))continue;let y=i.get(k.id).find(R=>R.id===h);l.set(k.id,{...u(y)}),p.push(k.id),d.push(k.id)}let m=new Map(d.map((h,k)=>[h,k])),f=new Float64Array(d.map(h=>l.get(h).x)),b=new Float64Array(d.map(h=>l.get(h).y)),g=new Float64Array(d.length),w=new Float64Array(d.length),S=d.map((h,k)=>i.get(h).flatMap(y=>{let R=m.get(y.id);if(R===void 0){let M=u(y);return g[k]+=M.x,w[k]+=M.y,[]}return[R]})),x=d.map(h=>i.get(h).length);for(let h=0;h<xa;h++){let k=0;for(let y=0;y<d.length;y++){let R=g[y],M=w[y];for(let A of S[y])R+=f[A],M+=b[A];let I=es*(R/x[y]-f[y]),G=es*(M/x[y]-b[y]);k=Math.max(k,Math.abs(I*o.scaleX)+Math.abs(G*o.scaleY)),f[y]+=I,b[y]+=G}if(k<Sa)break}d.forEach((h,k)=>{a[h]=n[h].map(()=>({x:f[k],y:b[k]}))});for(let[h,k]of Object.entries(n))a[h]??=k.map(y=>({...y}));return a}function Ra(e,t){let n=0,o=1/0;return e.forEach((s,r)=>{let a=(s.x-t.x)**2+(s.y-t.y)**2;a<o&&(o=a,n=r)}),n}function og(e,t,n,o){let s=(r,a)=>{let i=n[r],c=o[r];if(!i||!c||c.length===0)return{x:0,y:0};let l=Ra(c,a);return{x:i[l].x-c[l].x,y:i[l].y-c[l].y}};return Object.fromEntries(Object.entries(e).map(([r,a])=>{let i=t[Number(r)],c=s(i?.from??"",a[0]),l=s(i?.to??"",a.at(-1));return[r,a.map((u,p)=>{let d=a.length>1?p/(a.length-1):0;return{x:u.x+c.x+(l.x-c.x)*d,y:u.y+c.y+(l.y-c.y)*d}})]}))}function ts(e,t,{ids:n,alpha:o}){let s=(r,a)=>{for(let i=0;a&&i<a.count;i++){let c=r[a.start+i];c.color=Yn(c.color,o)}};for(let r of n)s(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:a},i)=>{(n.has(r)||n.has(a))&&(s(e.edgeCurves,e.edgeCurveRuns.get(i)),s(e.arrows,e.arrowRuns.get(i)))})}function va(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function rg(e,t,n,o){return!(e.referenceAxis||t.referenceAxis||e.pixelRows||t.pixelRows||t.tubeMap||o||n>ga)}function sg(){return typeof requestAnimationFrame<"u"&&!("matchMedia"in window&&window.matchMedia("(prefers-reduced-motion: reduce)").matches)}function ag(e,t,n){let o={frame:0,finish:()=>{e(1)}},s=0,r=performance.now(),a=()=>{if(!t()){n();return}let i=performance.now();s+=Math.min(i-r,wa),r=i;let c=Math.min(1,s/ba);e(va(c)),c<1?o.frame=requestAnimationFrame(a):n()};return o.frame=requestAnimationFrame(a),o}function ig(e,t,n,o){for(let[s,r]of Object.entries(e)){let a=t[s],i=n[s];!a||!i||r.forEach((c,l)=>{c.x=o===1?i[l].x:a[l].x+(i[l].x-a[l].x)*o,c.y=o===1?i[l].y:a[l].y+(i[l].y-a[l].y)*o})}}var Ma=8,La=19,ns=Ee+La,Na=48;function Pa(e,t,n){if(!(!e||!t))return at(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var Tg=Qr.views(e=>({get paneCeiling(){return Math.max(mt,e.paneHeight??oo)},get fitRoom(){return e.host?this.canvasHeight:this.paneCeiling},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=this.fitRoom,o=(e.walkRowGroups?.sections.length??0)*wo;return it(t.rows.length+1,n-this.fitPadTopBase-W-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?So(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return Pa(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=xe(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,s)=>({...o,y:t.rowY(s)})):n},get visibleRowLabels(){return this.drawnRowLabels.flatMap(({label:t,y:n})=>{let o=e.toScreen({x:0,y:n}).y;return o>=0&&o<=this.canvasHeight?[{label:t,y:n,top:o}]:[]})},get fitPadLeft(){return Math.max(W,...this.drawnRowLabels.map(t=>Fn(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ke(n,this.walkRowPitch):void 0;return t?Oe(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,s=o?t.reference:t.rows.find(r=>r.name===n);return s?{label:s.label,readout:Kn(s,o?void 0:t.reference,t.unit,s.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,s=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!s||!r)return;let a=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][a],c=r.rowY(a)*e.scaleY+e.translateY,l=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=s.barPx/2+2&&l>=0&&l<=i.bp?a:void 0},get fitPadTopBase(){let t=Wo(e.tubeMapGenes);return W+Math.max(0,t-1)*$o+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let s=this.fitPadTopBase,r=this.fitRoom,a=u=>(e.paneWidth-this.fitPadLeft-u)/t.w,i=u=>e.pixelRows?t.h+u+W<=r?1/0:0:(r-u-W)/t.h,c=Math.min(a(n+2*oe),i(s));return Math.min(a(W),i(s+o+oe))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+oe:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(W,e.legendSize.width+2*oe):W},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(so/o,(this.paneCeiling-this.fitPadTop-W)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?pt(t.map(s=>s.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?dt({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-ns)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=oe+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-Na?t+2*oe:Ma},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(mt,o.total+ns);let s=Math.max(mt,e.legendSize.height+2*oe+e.referenceStripZonePx),r=this.fitPads,a=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(s,t.h+a));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(s,t.h*Math.max(i/t.w,this.minFitScale)+a)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:J,top:J,right:J,bottom:J}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:W}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,s=this.fitPads;return t?Ce(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:s.left,padTop:s.top,padRight:s.right,padBottom:s.bottom}):void 0}})).views(e=>({viewportToBuild(){return eo(po(e),co)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,io]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=Ko();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:ro)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:s,layoutResult:r,deletionDrawing:a}=e;if(!o||!s||!r||!a)return;Be(e.viewportDirty,e.positionsVersion);let i=_t(()=>e.viewportToBuild()),c=st({...Ve(r,a,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:s,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:_t(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),l=e.morphEntering;return l?.layout===r&&ts(c,o.edges,l),{batch:c,viewportBounds:i}},get overlayLabels(){return Eo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Bo(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,s=t&&`${t.refName}:${t.start}-${t.end}`,r=we(e.sourceGfaLocation),a=n?.type==="GbzBaseSyntenyAdapter"?we(n.gbzDbLocation):void 0,i=r?{gfa:r,region:s}:a&&t&&s?{gbz:{db:a,index:we(n.haplotypeIndexLocation),region:s,haplotypes:e.cutHaplotypes?.map(d=>o?.[d]??d),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!i)return;let c=e.showGenes?e.geneTrack:void 0,l=c?e.sessionTrack(c.trackId):void 0,u=l?An(X(l,"adapter"),"gffGzLocation"):void 0,p=u?.type==="Gff3TabixAdapter"?{file:we(u.gffGzLocation),index:we(u.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...i,genes:p?.file&&p.index?p:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...pn({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.statedColorDomain}),walks:e.walkLayers.length?e.walkLayers.map(d=>d.color?d:d.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${Y(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base track or a GFA url":`bandage-figure draws no ${Y(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?fn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:e.drawsNodes?this.figureSpec():void 0}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var Mn=V(j("path",{d:"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z"}),"LineStyle");var os=V(j("path",{d:"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z"}),"CompareArrows");var rs=V(j("path",{d:"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2"}),"HighlightAlt");var Aa="Linear genome view",Ta="Linear synteny view",Ga="No synteny track in this session aligns these assemblies";function ss({label:e,icon:t,entries:n,entryLabel:o,onSelect:s,disabledHelpText:r,nameTheOnlyEntry:a=!0}){let[i]=n,c=r?[{label:e,icon:t,disabled:!0,disabledHelpText:r,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:a?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:s(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(l=>({label:o(l),onClick:s(l)}))}]}function jg({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:s}){let r=n[0]?.coverage??e.length;return[...ss({label:Aa,icon:Mn,entries:t,entryLabel:a=>`${a.sample} ${se(a)}`,onSelect:a=>()=>{o({location:a,assembly:a.sample})}}),...e.length>=2?ss({label:`${Ta} (${r} assemblies)`,icon:os,entries:n,entryLabel:a=>a.coverage<r?`${a.name} (${a.coverage} of ${r})`:a.name,nameTheOnlyEntry:!1,disabledHelpText:Ga,onSelect:a=>()=>{s(a.trackId)}}):[]]}function Yg({own:e,reference:t,highlight:n,onShowLinear:o,onHighlight:s}){let r=[e?{label:`Open in ${e.assembly} \u2014 ${se(e.location)}`,target:e}:void 0,t&&t.assembly!==e?.assembly?{label:`Open in ${t.assembly} \u2014 around this node`,target:t}:void 0].filter(a=>a!==void 0);return[...s&&n?[{label:`Highlight in ${n.assembly}`,icon:rs,onClick:()=>{s(n)}}]:[],...r.map(({label:a,target:i})=>({label:a,icon:Mn,onClick:()=>{o(i)}}))]}var qg=V(j("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var eb=V(j("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6"}),"Settings");var rb=V(j("path",{d:"M12 4.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5M12 17c-2.76 0-5-2.24-5-5s2.24-5 5-5 5 2.24 5 5-2.24 5-5 5m0-8c-1.66 0-3 1.34-3 3s1.34 3 3 3 3-1.34 3-3-1.34-3-3-3"}),"Visibility");export{V as a,hs as b,ke as c,xe as d,St as e,$s as f,Y as g,on as h,Xs as i,Vs as j,js as k,sn as l,an as m,se as n,Ys as o,gr as p,K as q,qs as r,cn as s,Wc as t,dn as u,Fc as v,Hc as w,Dc as x,Gr as y,rb as z,ng as A,og as B,rg as C,sg as D,ag as E,ig as F,xn as G,Vc as H,Zs as I,jc as J,ps as K,qo as L,ff as M,bf as N,kf as O,Ma as P,La as Q,ns as R,Tg as S,Mn as T,jg as U,Yg as V,qg as W,eb as X};
+//# sourceMappingURL=chunk-37IAMKOU.js.map