jbrowse-plugin-msaview 2.0.1 → 2.0.2

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Files changed (23) hide show
  1. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +3 -3
  2. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map +1 -1
  3. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts +1 -2
  4. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js +1 -2
  5. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map +1 -1
  6. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +2 -2
  7. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  8. package/dist/MsaViewPanel/model.d.ts +7 -16
  9. package/dist/MsaViewPanel/model.js +27 -19
  10. package/dist/MsaViewPanel/model.js.map +1 -1
  11. package/dist/jbrowse-plugin-msaview.umd.production.min.js +23 -23
  12. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  13. package/dist/utils/msa.js +31 -11
  14. package/dist/utils/msa.js.map +1 -1
  15. package/dist/utils/ncbiBlast.js +4 -4
  16. package/dist/utils/ncbiBlast.js.map +1 -1
  17. package/package.json +3 -2
  18. package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +3 -3
  19. package/src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx +1 -2
  20. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +2 -1
  21. package/src/MsaViewPanel/model.ts +25 -19
  22. package/src/utils/msa.ts +38 -8
  23. package/src/utils/ncbiBlast.ts +4 -4
package/dist/jbrowse-plugin-msaview.umd.production.min.js CHANGED
@@ -1,4 +1,4 @@
1
- "use strict";var JBrowsePluginMsaView=(()=>{var S2=Object.create;var Qo=Object.defineProperty;var x2=Object.getOwnPropertyDescriptor;var E2=Object.getOwnPropertyNames;var M2=Object.getPrototypeOf,O2=Object.prototype.hasOwnProperty;var C=(e,t)=>()=>(e&&(t=e(e=0)),t);var g=(e,t)=>()=>(t||e((t={exports:{}}).exports,t),t.exports),pt=(e,t)=>{for(var r in t)Qo(e,r,{get:t[r],enumerable:!0})},Zh=(e,t,r,n)=>{if(t&&typeof t=="object"||typeof t=="function")for(let i of E2(t))!O2.call(e,i)&&i!==r&&Qo(e,i,{get:()=>t[i],enumerable:!(n=x2(t,i))||n.enumerable});return e};var x=(e,t,r)=>(r=e!=null?S2(M2(e)):{},Zh(t||!e||!e.__esModule?Qo(r,"default",{value:e,enumerable:!0}):r,e)),A2=e=>Zh(Qo({},"__esModule",{value:!0}),e);var Jh=g((l$,Kh)=>{Kh.exports=JBrowseExports["@jbrowse/core/Plugin"]});var Le=g((c$,Qh)=>{Qh.exports=JBrowseExports["@jbrowse/core/util"]});var J=g((f$,qi)=>{function P2(e){return e&&e.__esModule?e:{default:e}}qi.exports=P2,qi.exports.__esModule=!0,qi.exports.default=qi.exports});var tm=g((d$,em)=>{em.exports=JBrowseExports["@mui/material/utils"]});var ee=g($c=>{"use strict";"use client";Object.defineProperty($c,"__esModule",{value:!0});Object.defineProperty($c,"default",{enumerable:!0,get:function(){return q2.createSvgIcon}});var q2=tm()});var te=g((h$,rm)=>{rm.exports=JBrowseExports["react/jsx-runtime"]});var nm=g(ea=>{"use strict";"use client";var k2=J();Object.defineProperty(ea,"__esModule",{value:!0});ea.default=void 0;var T2=k2(ee()),C2=te(),m$=ea.default=(0,T2.default)((0,C2.jsx)("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z"}),"GridOn")});var R=g((b$,om)=>{om.exports=JBrowseExports.react});var um=g((g$,am)=>{am.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes/ViewType"]});var zt=g((y$,sm)=>{sm.exports=JBrowseExports["mobx-state-tree"]});var Ht=g((w$,lm)=>{lm.exports=JBrowseExports.mobx});var D=g((S$,cm)=>{cm.exports=JBrowseExports["mobx-react"]});var B=g((x$,fm)=>{fm.exports=JBrowseExports["@mui/material"]});function R2(){let e=arguments.length>0&&arguments[0]!==void 0?arguments[0]:[],t=arguments.length>1&&arguments[1]!==void 0?arguments[1]:[];return e.length!==t.length||e.some((r,n)=>!Object.is(r,t[n]))}var $e,I2,Yc,ta,dm=C(()=>{"use client";$e=x(R()),I2=(0,$e.createContext)(null),Yc={didCatch:!1,error:null},ta=class extends $e.Component{constructor(t){super(t),this.resetErrorBoundary=this.resetErrorBoundary.bind(this),this.state=Yc}static getDerivedStateFromError(t){return{didCatch:!0,error:t}}resetErrorBoundary(){let{error:t}=this.state;if(t!==null){for(var r,n,i=arguments.length,o=new Array(i),a=0;a<i;a++)o[a]=arguments[a];(r=(n=this.props).onReset)===null||r===void 0||r.call(n,{args:o,reason:"imperative-api"}),this.setState(Yc)}}componentDidCatch(t,r){var n,i;(n=(i=this.props).onError)===null||n===void 0||n.call(i,t,r)}componentDidUpdate(t,r){let{didCatch:n}=this.state,{resetKeys:i}=this.props;if(n&&r.error!==null&&R2(t.resetKeys,i)){var o,a;(o=(a=this.props).onReset)===null||o===void 0||o.call(a,{next:i,prev:t.resetKeys,reason:"keys"}),this.setState(Yc)}}render(){let{children:t,fallbackRender:r,FallbackComponent:n,fallback:i}=this.props,{didCatch:o,error:a}=this.state,u=t;if(o){let p={error:a,resetErrorBoundary:this.resetErrorBoundary};if(typeof r=="function")u=r(p);else if(n)u=(0,$e.createElement)(n,p);else if(i===null||(0,$e.isValidElement)(i))u=i;else throw a}return(0,$e.createElement)(I2.Provider,{value:{didCatch:o,error:a,resetErrorBoundary:this.resetErrorBoundary}},u)}}});var Te=g((M$,pm)=>{pm.exports=JBrowseExports["@jbrowse/core/ui"]});async function wt(e,t,r){e.setError(void 0),t&&e.setMSAFilehandle(t),r&&e.setTreeFilehandle(r)}var Xc=C(()=>{});var hm,mm,vm,_m=C(()=>{hm=`CLUSTAL O(1.2.3) multiple sequence alignment
1
+ "use strict";var JBrowsePluginMsaView=(()=>{var q2=Object.create;var ra=Object.defineProperty;var k2=Object.getOwnPropertyDescriptor;var T2=Object.getOwnPropertyNames;var C2=Object.getPrototypeOf,j2=Object.prototype.hasOwnProperty;var C=(e,t)=>()=>(e&&(t=e(e=0)),t);var g=(e,t)=>()=>(t||e((t={exports:{}}).exports,t),t.exports),vt=(e,t)=>{for(var r in t)ra(e,r,{get:t[r],enumerable:!0})},rm=(e,t,r,n)=>{if(t&&typeof t=="object"||typeof t=="function")for(let i of T2(t))!j2.call(e,i)&&i!==r&&ra(e,i,{get:()=>t[i],enumerable:!(n=k2(t,i))||n.enumerable});return e};var x=(e,t,r)=>(r=e!=null?q2(C2(e)):{},rm(t||!e||!e.__esModule?ra(r,"default",{value:e,enumerable:!0}):r,e)),I2=e=>rm(ra({},"__esModule",{value:!0}),e);var im=g((m$,nm)=>{nm.exports=JBrowseExports["@jbrowse/core/Plugin"]});var Se=g((v$,om)=>{om.exports=JBrowseExports["@jbrowse/core/util"]});var Q=g((_$,ki)=>{function R2(e){return e&&e.__esModule?e:{default:e}}ki.exports=R2,ki.exports.__esModule=!0,ki.exports.default=ki.exports});var um=g((b$,am)=>{am.exports=JBrowseExports["@mui/material/utils"]});var oe=g(ef=>{"use strict";"use client";Object.defineProperty(ef,"__esModule",{value:!0});Object.defineProperty(ef,"default",{enumerable:!0,get:function(){return L2.createSvgIcon}});var L2=um()});var ae=g((y$,sm)=>{sm.exports=JBrowseExports["react/jsx-runtime"]});var lm=g(na=>{"use strict";"use client";var F2=Q();Object.defineProperty(na,"__esModule",{value:!0});na.default=void 0;var D2=F2(oe()),N2=ae(),w$=na.default=(0,D2.default)((0,N2.jsx)("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z"}),"GridOn")});var I=g((E$,fm)=>{fm.exports=JBrowseExports.react});var pm=g((O$,dm)=>{dm.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes/ViewType"]});var Ut=g((M$,hm)=>{hm.exports=JBrowseExports["mobx-state-tree"]});var Wt=g((A$,mm)=>{mm.exports=JBrowseExports.mobx});var D=g((P$,vm)=>{vm.exports=JBrowseExports["mobx-react"]});var N=g((q$,_m)=>{_m.exports=JBrowseExports["@mui/material"]});function H2(){let e=arguments.length>0&&arguments[0]!==void 0?arguments[0]:[],t=arguments.length>1&&arguments[1]!==void 0?arguments[1]:[];return e.length!==t.length||e.some((r,n)=>!Object.is(r,t[n]))}var Xe,z2,tf,ia,bm=C(()=>{"use client";Xe=x(I()),z2=(0,Xe.createContext)(null),tf={didCatch:!1,error:null},ia=class extends Xe.Component{constructor(t){super(t),this.resetErrorBoundary=this.resetErrorBoundary.bind(this),this.state=tf}static getDerivedStateFromError(t){return{didCatch:!0,error:t}}resetErrorBoundary(){let{error:t}=this.state;if(t!==null){for(var r,n,i=arguments.length,o=new Array(i),a=0;a<i;a++)o[a]=arguments[a];(r=(n=this.props).onReset)===null||r===void 0||r.call(n,{args:o,reason:"imperative-api"}),this.setState(tf)}}componentDidCatch(t,r){var n,i;(n=(i=this.props).onError)===null||n===void 0||n.call(i,t,r)}componentDidUpdate(t,r){let{didCatch:n}=this.state,{resetKeys:i}=this.props;if(n&&r.error!==null&&H2(t.resetKeys,i)){var o,a;(o=(a=this.props).onReset)===null||o===void 0||o.call(a,{next:i,prev:t.resetKeys,reason:"keys"}),this.setState(tf)}}render(){let{children:t,fallbackRender:r,FallbackComponent:n,fallback:i}=this.props,{didCatch:o,error:a}=this.state,u=t;if(o){let f={error:a,resetErrorBoundary:this.resetErrorBoundary};if(typeof r=="function")u=r(f);else if(n)u=(0,Xe.createElement)(n,f);else if(i===null||(0,Xe.isValidElement)(i))u=i;else throw a}return(0,Xe.createElement)(z2.Provider,{value:{didCatch:o,error:a,resetErrorBoundary:this.resetErrorBoundary}},u)}}});var qe=g((T$,gm)=>{gm.exports=JBrowseExports["@jbrowse/core/ui"]});async function Ot(e,t,r){e.setError(void 0),t&&e.setMSAFilehandle(t),r&&e.setTreeFilehandle(r)}var rf=C(()=>{});var ym,wm,Sm,xm=C(()=>{ym=`CLUSTAL O(1.2.3) multiple sequence alignment
2
2
  UniProt/Swiss-Prot|P26898|IL2RA_SHEEP MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
3
3
  UniProt/Swiss-Prot|P01590|IL2RA_MOUSE MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
4
4
  UniProt/Swiss-Prot|P41690|IL2RA_FELCA MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
@@ -11,7 +11,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE PLPLRSLLFLQLPLLGVGLNP----------------
11
11
  UniProt/Swiss-Prot|P36835|IL2_CAPHI -----------LLGVGLNPKFLTP------------------------------------
12
12
  UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
13
13
  UniProt/Swiss-Prot|Q29416|IL2_CANFA --------------LFLQLSLLG-------------------------------------
14
- `,mm=`CLUSTAL O(1.2.4) multiple sequence alignment
14
+ `,wm=`CLUSTAL O(1.2.4) multiple sequence alignment
15
15
 
16
16
 
17
17
  sp|P69905|HBA_HUMAN MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG 60
@@ -27,35 +27,35 @@ sp|P13786|HBAZ_CAPHI SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
27
27
  sp|P69905|HBA_HUMAN AVHASLDKFLASVSTVLTSKYR 142
28
28
  sp|P01942|HBA_MOUSE AVHASLDKFLASVSTVLTSKYR 142
29
29
  sp|P13786|HBAZ_CAPHI DAHAAWDKFLSIVSGVLTEKYR 142
30
- .**: ****: ** ***.***`,vm="(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)"});var Fe,ra,bm,Vt,L2,gm,ym=C(()=>{Fe=x(R()),ra=x(B()),bm=x(D());_m();Xc();Vt=({onClick:e,model:t,children:r})=>Fe.default.createElement("li",null,Fe.default.createElement(ra.Link,{onClick:n=>{t.setError(void 0),n.preventDefault(),e()},href:"#"},Fe.default.createElement(ra.Typography,{display:"inline"},r))),L2=(0,bm.observer)(function({model:e}){return Fe.default.createElement("ul",null,Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,void 0,{uri:"https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh",locationType:"UriLocation"})},"230k COVID-19 samples (tree only)"),Fe.default.createElement(Vt,{model:e,onClick:()=>{e.setData({msa:hm,tree:vm})}},"Small protein MSA+tree"),Fe.default.createElement(Vt,{model:e,onClick:()=>{e.setData({msa:mm})}},"Small MSA only"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock",locationType:"UriLocation"})},"PFAM SARS-CoV2 multi-stockholm"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock",locationType:"UriLocation"})},"Lysine stockholm file"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt",locationType:"UriLocation"})},"PF01601 stockholm file (SARS-CoV2 spike protein)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa",locationType:"UriLocation"})},"Europe COVID full genomes (LR883044.1 and 199 other sequences)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa",locationType:"UriLocation"},{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh",locationType:"UriLocation"})},"MAFFT+VeryFastTree(17.9k samples)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/demos/ttc39a.mfa",locationType:"UriLocation"})},"Human BLAST results mfa"))}),gm=L2});var se,wm,Me,Zc,Sm,xm=C(()=>{se=x(R()),wm=x(D()),Me=x(B()),Zc=x(Te());Xc();ym();Sm=(0,wm.observer)(({model:e})=>{let[t,r]=(0,se.useState)(),[n,i]=(0,se.useState)(),{error:o}=e;return se.default.createElement(Me.Container,null,se.default.createElement("div",{style:{width:"50%"}},o?se.default.createElement("div",{style:{padding:20}},se.default.createElement(Me.Typography,{color:"error"},"Error: ",`${o}`)):null,se.default.createElement(Me.Typography,null,"Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),se.default.createElement(Me.Typography,{color:"error"},"Note: you can open up just an MSA or just a tree, both are not required. 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r=t.quiet?()=>null:kV,n=t.strict?ar:r,i=[],o=null;return e.split(`
38
+ `).forEach((u,f)=>{let l=()=>{o||(n(yc(f)+$x),o=new le)},d;Xx.test(u)?(o&&n(yc(f)+MV),o=new le):gV.test(u)?(o?i.push(o):n(yc(f)+$x),o=null):(d=yV.exec(u))?(l(),o.gf[d[1]]=o.gf[d[1]]||[],o.gf[d[1]].push(d[2])):(d=wV.exec(u))?(l(),o.gc[d[1]]=o.gc[d[1]]||"",o.gc[d[1]]+=d[2]):(d=SV.exec(u))?(l(),o.gs[d[2]]=o.gs[d[2]]||{},o.gs[d[2]][d[1]]=o.gs[d[2]][d[1]]||[],o.gs[d[2]][d[1]].push(d[3])):(d=xV.exec(u))?(l(),o.gr[d[2]]=o.gr[d[2]]||{},o.gr[d[2]][d[1]]=o.gr[d[2]][d[1]]||"",o.gr[d[2]][d[1]]+=d[3]):(d=EV.exec(u))?(l(),o.seqdata[d[1]]||(o.seqdata[d[1]]="",o.seqname.push(d[1])),o.seqdata[d[1]]+=d[2]):OV.test(u)&&ar(yc(f)+AV)}),o&&(n("Warning: no end line //"),i.push(o)),i},TV=(e,t)=>{let r=Gp(e,t);return r.length===0&&ar("No alignments found"),r.length>1&&ar("More than one alignment found"),r[0]},CV=(e,t)=>{let r=new le;return t=t||Object.keys(e),t.forEach(n=>r.addRow(n,e[n])),r},jV=e=>{let t=new le;return e.forEach(r=>t.addRow(r[0],r[1])),t};le.prototype.rows=function(){return this.seqname.length};le.prototype.columns=function(){let e=0;return this.seqname.forEach(t=>{e=Math.max(e,this.seqdata[t].length)}),Object.keys(this.gr).forEach(t=>Object.keys(this.gr[t]).forEach(r=>{e=Math.max(e,this.gr[t][r].length)})),e};le.prototype.allNames=function(){let e={},t=[],r=i=>{e[i]||(e[i]=!0,t.push(i))},n=i=>i.forEach(r);return n(this.seqname),n(Object.keys(this.seqdata)),Object.keys(this.gr).forEach(i=>n(Object.keys(this.gr[i]))),Object.keys(this.gs).forEach(i=>n(Object.keys(this.gs[i]))),t};le.prototype.allTags=function(){let e={},t=r=>Object.keys(r).forEach(n=>e[n]=!0);return t(this.gc),t(this.gf),t(this.gr),t(this.gs),Object.keys(e).sort()};le.prototype.addRow=function(e,t){return this.seqdata[e]&&ar("Duplicate row name"),this.seqname.push(e),this.seqdata[e]=t||"",this};le.prototype.deleteRow=function(e){return this.seqdata[e]||ar("Row not found"),this.seqname=this.seqname.filter(t=>t!==e),delete this.seqdata[e],Object.keys(this.gr).forEach(t=>delete this.gr[t][e]),Object.keys(this.gs).forEach(t=>delete this.gs[t][e]),this};var Sc=(e,t)=>{let r={};return Object.keys(e).forEach(n=>r[n]=t(e[n])),r},Mo=e=>Sc(e,t=>t.slice(0)),Vp=e=>Sc(e,t=>Mo(t));le.prototype.copy=function(){let e=new le;return e.seqname=this.seqname.slice(0),e.seqdata=Mo(this.seqdata),e.gf=Mo(this.gf),e.gc=Mo(this.gc),e.gs=Vp(this.gs),e.gr=Vp(this.gr),e};var IV=(e,t)=>t.map(r=>e[r]).join(""),Up=(e,t)=>Sc(e,r=>IV(r,t)),RV=(e,t)=>Sc(e,r=>Up(r,t));le.prototype.extractColumns=function(e){let t=this.columns(),r=e.filter(i=>i<0||i>=t);r.length&&ar("Bad column indices: "+r.join(","));let n=new le;return n.seqname=this.seqname.slice(0),n.seqdata=Up(this.seqdata,e),n.gf=Mo(this.gf),n.gc=Up(this.gc,e),n.gs=Vp(this.gs),n.gr=RV(this.gr,e),n};le.prototype.extractColumnRange=function(e,t){return this.extractColumns(new Array(t+1-e).fill(0).map((r,n)=>e+n))};le.prototype.defaultGapChars=".-";le.prototype.seqpos2col=function(e,t){t=t||this.defaultGapChars,this.seqdata[e]||ar("Row not found");let r=this.seqdata[e];return r.split("").map((n,i)=>t.indexOf(r[i])<0?i:-1).filter(n=>n>=0)};le.prototype.col2seqpos=function(e,t){t=t||this.defaultGapChars,this.seqdata[e]||ar("Row not found");let r=this.seqdata[e],n=-1;return r.split("").map((i,o)=>t.indexOf(r[o])<0?++n:n+.5)};function wc(e,t){for(;e.length<t;)e=" "+e;return e}function Yx(e,t){for(;e.length<t;)e=e+" ";return e}function LV(e){return wc("",e)}le.prototype.toString=function(e){e=e||{width:80,indentNames:!1};let t=this.allNames(),r=this.columns(),n=Math.max.apply(null,t.map(d=>d.length).concat([0])),i=Math.max.apply(null,this.allTags().map(d=>d.length).concat([0])),o=i?i+6:0,a=e.width?Math.max(1,e.width-n-o-1):r,u=e.indentNames?wc:Yx,f=e.indentNames?(d,s)=>wc(d,i)+" "+wc(s,n):(d,s)=>Yx(d+" "+s,i+n+1),l=[0];for(let d=a;d<r;d+=a)l.push(d);return`# STOCKHOLM 1.0
37
39
  `+Object.keys(this.gf).sort().map(d=>this.gf[d].map(s=>"#=GF "+u(d,i)+" "+s+`
38
- `).join("")).join("")+Object.keys(this.gs).sort().map(d=>Object.keys(this.gs[d]).map(s=>this.gs[d][s].map(c=>"#=GS "+p(d,s)+" "+c+`
39
- `).join("")).join("")).join("")+l.map(d=>Object.keys(this.gc).sort().map(s=>"#=GC "+u(s,i)+qV(n+2)+this.gc[s].substr(d,a)+`
40
- `).join("")+t.map(s=>Object.keys(this.gr).filter(c=>this.gr[c][s]).sort().map(c=>"#=GR "+p(c,s)+" "+this.gr[c][s].substr(d,a)+`
40
+ `).join("")).join("")+Object.keys(this.gs).sort().map(d=>Object.keys(this.gs[d]).map(s=>this.gs[d][s].map(c=>"#=GS "+f(d,s)+" "+c+`
41
+ `).join("")).join("")).join("")+l.map(d=>Object.keys(this.gc).sort().map(s=>"#=GC "+u(s,i)+LV(n+2)+this.gc[s].substr(d,a)+`
42
+ `).join("")+t.map(s=>Object.keys(this.gr).filter(c=>this.gr[c][s]).sort().map(c=>"#=GR "+f(c,s)+" "+this.gr[c][s].substr(d,a)+`
41
43
  `).join("")+(this.seqdata[s]?u(s,n+o)+" "+this.seqdata[s].substr(d,a)+`
42
44
  `:"")).join("")).join(`
43
45
  `)+`//
44
- `};ue.prototype.toFasta=function(e){e=e||{width:80};let t=this.columns(),r=e.width||t,n=[0];for(let i=r;i<t;i+=r)n.push(i);return this.allNames().map(i=>this.seqdata[i]?">"+i+`
46
+ `};le.prototype.toFasta=function(e){e=e||{width:80};let t=this.columns(),r=e.width||t,n=[0];for(let i=r;i<t;i+=r)n.push(i);return this.allNames().map(i=>this.seqdata[i]?">"+i+`
45
47
  `+n.map(o=>this.seqdata[i].substr(o,r)+`
46
- `).join(""):"").join("")};ue.prototype.toRowList=function(e){return this.allNames().filter(t=>this.seqdata[t]).map(t=>[t,this.seqdata[t]])};typeof Rp<"u"&&(Rp.exports={sniff:wV,validate:SV,parse:EV,parseAll:Lp,fromSeqIndex:MV,fromRowList:OV,Stockholm:ue})});var Fp=g((Mte,Lx)=>{Lx.exports=Rx()});var Fx=g((Dp,Np)=>{(function(e,t){typeof define=="function"&&define.amd?define([],t):typeof Dp<"u"?t():(t(),e.FileSaver={})})(Dp,function(){"use strict";function e(u,p){return typeof p>"u"?p={autoBom:!1}:typeof p!="object"&&(console.warn("Deprecated: Expected third argument to be a object"),p={autoBom:!p}),p.autoBom&&/^\s*(?:text\/\S*|application\/xml|\S*\/\S*\+xml)\s*;.*charset\s*=\s*utf-8/i.test(u.type)?new Blob(["\uFEFF",u],{type:u.type}):u}function t(u,p,l){var d=new XMLHttpRequest;d.open("GET",u),d.responseType="blob",d.onload=function(){a(d.response,p,l)},d.onerror=function(){console.error("could not download file")},d.send()}function r(u){var p=new 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i=n.seqs.map((a,u)=>({id:n.ids[u],seq:a})),{consensus:o}=n;if(o.length!=i[0].seq.length)throw new Error(`Consensus length != sequence length. 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+ `)[Symbol.iterator]());if(t===void 0)throw new Error("No blocks parsed");let r=t.seqs.map((i,o)=>({id:t.ids[o],seq:i})),{consensus:n}=t;if(n.length!=r[0].seq.length)throw new Error(`Consensus length != sequence length. Con ${n.length} seq ${r[0].seq.length}`);return{consensus:n,alns:r}}Nt.parsePairwiseIter=bE;function UV(e){let t=e.split(`
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+ `)[Symbol.iterator]();return _E(t)}Nt.parse=UV;function WV(e){let t=e.split(`
49
51
  `).filter(r=>!r.startsWith("#")).join(`
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of r)for(let i=0;i<n.length;i++){let o=t[i]||{};o[n[i]]||(o[n[i]]=0),o[n[i]]++,t[i]=o}return t},get hierarchy(){let t=this.root;return Cp().size([this.totalHeight,e.treeWidth]).separation(()=>1)(t),pp(t,t.data.length=0,e.treeWidth/hp(t)),t},get totalHeight(){return this.root.leaves().length*e.rowHeight}})).views(e=>({get totalWidth(){return e.numColumns*e.colWidth}})).views(e=>({get initialized(){return(e.data.msa||e.data.tree)&&!e.error},get blocksX(){return Ux({viewportWidth:e.msaAreaWidth,viewportX:-e.scrollX,blockSize:e.blockSize,mapWidth:e.totalWidth})},get blocksY(){return Vx({viewportHeight:e.height,viewportY:-e.scrollY,blockSize:e.blockSize,mapHeight:e.totalHeight})}})).views(e=>({get blocks2d(){let t=[];for(let r of e.blocksY)for(let n of e.blocksX)t.push([n,r]);return t},get isLoading(){return e.loadingMSA||e.loadingTree},get maxScrollX(){return-e.totalWidth+(e.msaAreaWidth-100)}})).actions(e=>({zoomIn(){e.colWidth=Math.ceil(e.colWidth*1.5),e.rowHeight=Math.ceil(e.rowHeight*1.5),e.scrollX=si(e.maxScrollX,e.scrollX,0)},zoomOut(){e.colWidth=Math.max(1,Math.floor(e.colWidth*.75)),e.rowHeight=Math.max(1.5,Math.floor(e.rowHeight*.75)),e.scrollX=si(e.maxScrollX,e.scrollX,0)},setLoadedInterProAnnotations(t){e.loadedInterProAnnotations=t},doScrollY(t){e.scrollY=si(-e.totalHeight+10,e.scrollY+t,0)},doScrollX(t){e.scrollX=si(e.maxScrollX,e.scrollX+t,0)},setScrollX(t){e.scrollX=si(e.maxScrollX,t,0)},toggleTrack(t){e.turnedOffTracks.has(t)?e.turnedOffTracks.delete(t):e.turnedOffTracks.set(t,!0)},addInterProScanJobId(t){e.interProScanJobIds=[...e.interProScanJobIds,{jobId:t,date:+Date.now()}]},setStatus(t){e.status=t}})).views(e=>({get labelsWidth(){let t=0,{rowHeight:r,hierarchy:n,treeMetadata:i,fontSize:o}=e;if(r>5)for(let a of n.leaves())t=Math.max(Gx(i[a.data.name]?.genome||a.data.name,o),t);return t},get secondaryStructureConsensus(){return e.MSA?.secondaryStructureConsensus},get seqConsensus(){return e.MSA?.seqConsensus},get conservation(){if(e.columns2d.length)for(let t=0;t<e.columns2d[0].length;t++){let r=[];for(let n of e.columns2d)r.push(n[t])}return["a"]},get adapterTrackModels(){return e.MSA?.tracks.map(t=>({model:{...t,data:t.data?dp(e.blanks,t.data):void 0,height:e.rowHeight},ReactComponent:Xx}))||[]},get tracks(){return this.adapterTrackModels},get turnedOnTracks(){return this.tracks.filter(t=>!e.turnedOffTracks.has(t.model.id))},globalCoordToRowSpecificSeqCoord(t,r){let{rowNames:n,rows:i}=e,o=n.indexOf(t);if(o!==-1&&i[o]){let a=i[o][1],u=0;for(let p=0;p<r;p++)if(a[p]!=="-")u++;else if(u>=r)break;return u}return 0},seqCoordToRowSpecificGlobalCoord(t,r){let{rowNames:n,rows:i}=e,o=n.indexOf(t);if(o!==-1&&i[o]){let a=i[o][1],u=0,p=0;for(;u<r;p++)if(a[p]!=="-")u++;else if(u>=r)break;return p}return 0}})).views(e=>({get totalTrackAreaHeight(){return(0,Rt.sum)(e.turnedOnTracks.map(t=>t.model.height))},get tidyTypes(){let t=new Map;if(this.tidyAnnotations)for(let{name:r,accession:n,description:i}of this.tidyAnnotations)t.set(n,{name:r,accession:n,description:i});return t},get tidyAnnotations(){let t=[],{loadedInterProAnnotations:r}=e;if(r)for(let[n,i]of Object.entries(r))for(let{signature:o,locations:a}of i.matches){let{entry:u}=o;if(u){let{name:p,accession:l,description:d}=u;for(let{start:s,end:c}of a)t.push({id:n,name:p,accession:l,description:d,start:s,end:c})}}return t.sort((n,i)=>vp(i)-vp(n))},get tidyFilteredAnnotations(){return this.tidyAnnotations.filter(t=>e.featureFilters.get(t.accession))},get tidyFilteredGatheredAnnotations(){return(0,Rt.groupBy)(this.tidyFilteredAnnotations,t=>t.id)}})).views(e=>({get fillPalette(){let t=[...e.tidyTypes.keys()],r=0,n={};for(let i of t){let o=Math.min(t.length-1,yp.length-1);n[i]=yp[o][r],r++}return n},get strokePalette(){return Object.fromEntries(Object.entries(this.fillPalette).map(([t,r])=>[t,Ce(r).darken(.1).toHex()]))}})).actions(e=>({async loadInterProScanResults(t){e.setStatus({msg:"Loading "+t});let r=await Zp(t);e.setStatus(),e.setLoadedInterProAnnotations(Object.fromEntries(r.results.map(n=>[n.xref[0].id,n])))},async queryInterProScan(t){let{rows:r}=e;if(r.length>140)throw new Error("Too many sequences, please run InterProScan offline");let n=await EE({algorithm:"interproscan",programs:t,seq:r.map(i=>`>${i[0]}
52
- ${i[1].replaceAll("-","")}`).join(`
53
- `),onProgress:i=>e.setStatus(i),onJobId:i=>e.addInterProScanJobId(i)});e.setLoadedInterProAnnotations(Object.fromEntries(n.results.map(i=>[i.xref[0].id,i])))},reset(){(0,gt.transaction)(()=>{e.setData({tree:"",msa:""}),e.setScrollY(0),e.setScrollX(0),e.setCurrentAlignment(0),e.setTreeFilehandle(void 0),e.setMSAFilehandle(void 0)})},async exportSVG(t){let{renderToSvg:r}=await Promise.resolve().then(()=>(BE(),NE)),n=await r(e,t),i=new Blob([n],{type:"image/svg+xml"});(0,HE.saveAs)(i,"image.svg")},incrementRef(){e.nref++},initFilter(t){e.featureFilters.get(t)===void 0&&e.featureFilters.set(t,!0)},setFilter(t,r){e.featureFilters.set(t,r)},afterCreate(){(0,X.addDisposer)(e,(0,gt.autorun)(()=>{for(let t of e.tidyTypes.keys())this.initFilter(t)})),(0,X.addDisposer)(e,(0,gt.autorun)(async()=>{})),(0,X.addDisposer)(e,(0,gt.autorun)(async()=>{let{treeFilehandle:t}=e;if(t)try{e.setLoadingTree(!0),e.setTree(await(0,gc.openLocation)(t).readFile("utf8")),t.locationType==="BlobLocation"&&e.setTreeFilehandle(void 0)}catch(r){console.error(r),e.setError(r)}finally{e.setLoadingTree(!1)}})),(0,X.addDisposer)(e,(0,gt.autorun)(async()=>{let{treeMetadataFilehandle:t}=e;if(t)try{e.setTreeMetadata(await(0,gc.openLocation)(t).readFile("utf8"))}catch(r){console.error(r),e.setError(r)}})),(0,X.addDisposer)(e,(0,gt.autorun)(async()=>{let{msaFilehandle:t}=e;if(t)try{e.setLoadingMSA(!0);let r=await(0,gc.openLocation)(t).readFile("utf8");(0,gt.transaction)(()=>{e.setMSA(r),t.locationType==="BlobLocation"&&e.setMSAFilehandle(void 0)})}catch(r){console.error(r),e.setError(r)}finally{e.setLoadingMSA(!1)}})),(0,X.addDisposer)(e,(0,gt.autorun)(async()=>{e.treeWidthMatchesArea&&e.setTreeWidth(Math.max(50,e.treeAreaWidth-e.labelsWidth-10-e.marginLeft))})),(0,X.addDisposer)(e,(0,gt.autorun)(()=>{(0,Rt.localStorageSetItem)("msaview-interproscanqueries",JSON.stringify(e.interProScanJobIds))}))}})).postProcessSnapshot(e=>{let t=e,{data:{tree:r,msa:n,treeMetadata:i},...o}=t;return{data:{...e.treeFilehandle?{}:{tree:r},...e.msaFilehandle?{}:{msa:n},...e.treeMetadataFilehandle?{}:{treeMetadata:i}},...o}})}var gt,X,zE,HE,mi,gc,Rt,Qp,VE=C(()=>{gt=x(Ht()),X=x(zt());Tx();fp();zE=x(Fp()),HE=x(Fx()),mi=x(Nx()),gc=x(zx()),Rt=x(Le());an();Bl();Hx();Wx();$x();wp();Zx();aE();sE();lE();$p();Gl();fE();hE();vE();gE();ME();Qp=YV});var eh=C(()=>{rx();VE()});var WE=g((Are,UE)=>{UE.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes"]});async function GE(e,t){let r=await fetch(e,t);if(!r.ok)throw new Error(`HTTP ${r.status} fetching ${e} ${await r.text()}`);return r}async function Ue(e,t){return(await GE(e,t)).text()}async function $E(e,t){return(await GE(e,t)).json()}function yc(e){return new Promise(t=>setTimeout(t,e))}var th=C(()=>{"use strict"});async function XE({query:e,blastDatabase:t,blastProgram:r,onProgress:n,onRid:i}){n("Submitting to NCBI BLAST...");let{rid:o}=await JV({query:e,blastDatabase:t,blastProgram:r});i(o),await QV({rid:o,onProgress:n});let u=(await $E(`${qo}?CMD=Get&RID=${o}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`)).BlastOutput2[0].report.results.search.hits;return{rid:o,hits:u}}async function JV({query:e,blastProgram:t,blastDatabase:r}){let n=await Ue(qo,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{}})}),i=n.match(/^ RID = (.*$)/m)?.[1],o=n.match(/^ RTOE = (.*$)/m)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:o}}async function QV({rid:e,onProgress:t}){for(;;){for(let i=0;i<20;i++)await yc(1e3),t(`Re-checking BLAST status in... ${20-i}`);let n=await Ue(`${qo}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`);if(!n.match(/\s+Status=WAITING/m)){if(n.match(/\s+Status=FAILED/m))throw new Error(`BLAST ${e} failed; please report to blast-help@ncbi.nlm.nih.gov`);if(n.match(/\s+Status=READY/m)){if(n.match(/\s+ThereAreHits=yes/m))return!0;throw new Error("No hits found")}}}}var qo,nh=C(()=>{"use strict";th();qo="https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi"});var rM=g(Sc=>{"use strict";Object.defineProperty(Sc,"__esModule",{value:!0});Sc.genomeToTranscriptSeqMapping=void 0;function eU(e){var t,r;let n=e.strand,i=e.refName,o=(r=(t=e.subfeatures)===null||t===void 0?void 0:t.filter(l=>l.type==="CDS").sort((l,d)=>n*(l.start-d.start)))!==null&&r!==void 0?r:[],a={},u={},p=0;if(n!==-1)for(let l of o)for(let d=l.start;d<l.end;d++){let s=Math.floor(p++/3);a[d]=s,u[s]||(u[s]=d)}else for(let l of o)for(let d=l.end;d>l.start;d--){let s=Math.floor(p++/3);a[d]=s,u[s]||(u[s]=d)}return{g2p:a,p2g:u,refName:i,strand:n}}Sc.genomeToTranscriptSeqMapping=eU});function oh(e){return Ec.default.createElement(oM.SvgIcon,{...e},Ec.default.createElement("path",{d:"M0 0h24v24H0z",fill:"none"}),Ec.default.createElement("path",{d:"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"}))}var Ec,oM,aM=C(()=>{"use strict";Ec=x(R()),oM=x(B())});function tU({rid:e}){return Mc.default.createElement(Oc.Typography,null,"RID ",e," ",Mc.default.createElement(Oc.Link,{target:"_black",href:`${qo}?CMD=Get&RID=${e}`},"(see status at NCBI ",Mc.default.createElement(oh,null),")"))}var Mc,Oc,ah,uM=C(()=>{"use strict";Mc=x(R()),Oc=x(B());aM();nh();ah=tU});function rU({rid:e,error:t}){return st.default.createElement("div",null,e?st.default.createElement(ah,{rid:e}):null,st.default.createElement(Ac.ErrorMessage,{error:t}))}function nU({rid:e,progress:t}){let{classes:r}=cM();return st.default.createElement("div",{className:r.loading},e?st.default.createElement(ah,{rid:e}):null,st.default.createElement(uh.Typography,null,t))}var st,uh,sM,lM,Ac,cM,iU,fM,dM=C(()=>{"use strict";st=x(R()),uh=x(B()),sM=x(D()),lM=x(St()),Ac=x(Te());uM();cM=(0,lM.makeStyles)()(e=>({margin:{padding:20},loading:{background:e.palette.background.paper}}));iU=(0,sM.observer)(function({model:t}){let{progress:r,rid:n,error:i,processing:o}=t,{classes:a}=cM();return st.default.createElement("div",{className:a.margin},st.default.createElement(Ac.LoadingEllipses,{message:"Running NCBI BLAST",variant:"h5"}),i?st.default.createElement(rU,{rid:n,error:i}):n?st.default.createElement(nU,{rid:n,progress:r}):null,st.default.createElement(uh.Typography,null,o||"Initializing BLAST query"))}),fM=iU});var hM={};pt(hM,{default:()=>aU});var Pc,pM,oU,aU,mM=C(()=>{"use strict";Pc=x(R()),pM=x(D());eh();dM();oU=(0,pM.observer)(function({model:t}){let{blastParams:r}=t;return Pc.default.createElement("div",null,r?Pc.default.createElement(fM,{model:t}):Pc.default.createElement(Tp,{model:t}))}),aU=oU});var bM=g(qc=>{"use strict";"use client";var sU=J();Object.defineProperty(qc,"__esModule",{value:!0});qc.default=void 0;var lU=sU(ee()),cU=te(),une=qc.default=(0,lU.default)((0,cU.jsx)("path",{d:"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z"}),"Add")});var xM=g((pne,SM)=>{SM.exports=JBrowseExports["@jbrowse/core/configuration"]});var u$={};pt(u$,{default:()=>Gc});var g2=x(Jh()),y2=x(Le()),w2=x(nm());var im="2.0.1";var vM=x(R()),_M=x(um());var me=x(zt()),xc=x(Ht());eh();var vi=x(Le()),nM=x(WE());th();var Lt="https://www.ebi.ac.uk/Tools/services/rest";async function XV({sequence:e,onProgress:t}){let r=await Ue(`${Lt}/clustalo/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",sequence:e})});return await rh({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Ue(`${Lt}/clustalo/result/${r}/aln-clustal_num`),tree:await Ue(`${Lt}/clustalo/result/${r}/phylotree`)}}async function ZV({sequence:e,onProgress:t}){let r=await Ue(`${Lt}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await rh({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Ue(`${Lt}/muscle/result/${r}/fa`),tree:await Ue(`${Lt}/muscle/result/${r}/phylotree`)}}async function KV({sequence:e,onProgress:t}){let r=await Ue(`${Lt}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await rh({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Ue(`${Lt}/kalign/result/${r}/fa`),tree:await Ue(`${Lt}/kalign/result/${r}/phylotree`)}}async function rh({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let i=0;i<10;i++)await yc(1e3),e(`Re-checking MSA status in... ${10-i}`);if(await Ue(`${Lt}/${r}/status/${t}`)==="FINISHED")break}}async function YE({algorithm:e,sequence:t,onProgress:r}){if(r(`Launching ${e} MSA...`),e==="clustalo")return XV({sequence:t,onProgress:r});if(e==="muscle")return ZV({sequence:t,onProgress:r});if(e==="kalign")return KV({sequence:t,onProgress:r});throw new Error("unknown algorithm")}nh();function ZE(e){return`${e.accession}-${e.sciname.replaceAll(" ","_")}`}function KE(e){return e.replace("-","")}async function JE({self:e}){let{blastDatabase:t,blastProgram:r,msaAlgorithm:n,proteinSequence:i}=e.blastParams,o=i.replaceAll("*","").replaceAll("&",""),{hits:a}=await XE({query:o,blastDatabase:t,blastProgram:r,onProgress:l=>e.setProgress(l),onRid:l=>e.setRid(l)}),u=[`>QUERY
54
- ${o}`,...a.map(l=>[ZE(l.description[0]),KE(l.hsps[0].hseq)]).map(([l,d])=>`>${l}
52
+ `);return bE(t)}Nt.parsePairwise=WV});var yE,Ao,wE=C(()=>{yE=x(gE()),Ao=class{MSA;constructor(t){this.MSA=(0,yE.parse)(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.alns.find(r=>r.id===t)?.seq||""}getWidth(){return this.MSA.alns[0].seq.length}getRowData(){}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,branchset:this.getNames().map(t=>({id:t,name:t,branchset:[]}))}}get seqConsensus(){return this.MSA.consensus}get secondaryStructureConsensus(){}get tracks(){return[]}}});function Po(e){let t=[],r={},n=e.split(/\s*(;|\(|\)|,|:)\s*/);for(let i=0;i<n.length;i++){let o=n[i],a={};switch(o){case"(":r.branchset=[a],t.push(r),r=a;break;case",":t.at(-1)?.branchset.push(a),r=a;break;case")":r=t.pop();break;case":":break;default:{let u=n[i-1];u===")"||u==="("||u===","?r.name=o:u===":"&&(r.length=parseFloat(o))}}}return r}var nh=C(()=>{});var SE,qo,xE=C(()=>{SE=x($p());nh();ln();qo=class{data;MSA;constructor(t,r){let n=SE.default.parseAll(t);this.data=n,this.MSA=n[r]}getMSA(){return this.MSA}getRow(t){return this.MSA?.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA?.seqdata)[0];return this.getRow(t).length}get alignmentNames(){return this.data.map((t,r)=>t.gf.DE?.[0]||`Alignment ${r+1}`)}getHeader(){return{General:this.MSA.gf,Accessions:this.MSA.gs?.AC,Dbxref:this.MSA.gs?.DR}}getRowData(t){return{name:t,accession:this.MSA.gs?.AC?.[t],dbxref:this.MSA.gs?.DR?.[t]}}getNames(){return Object.keys(this.MSA.seqdata)}getSeqCoords(){}getStructures(){let t=/PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/,r=this.MSA,n=Object.entries(r.gs?.DR||{}).map(([o,a])=>[o,t.exec(a)]).filter(o=>!!o[1]).map(([o,a])=>{let u=a[1].toLowerCase(),f=a[2],l=+a[3],d=+a[4];return{id:o,pdb:u,chain:f,startPos:l,endPos:d}}),i={};for(let o of n){let{id:a,...u}=o;i[a]||(i[a]=[]),i[a].push(u)}return i}getTree(){let t=this.MSA?.gf?.NH?.[0];return t?bo(Po(t)):{id:"root",name:"root",noTree:!0,branchset:this.getNames().map(r=>({id:r,branchset:[],name:r}))}}get seqConsensus(){return this.MSA.gc?.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc?.SS_cons}get tracks(){return[{id:"seqConsensus",name:"Sequence consensus",data:this.seqConsensus,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:this.secondaryStructureConsensus,customColorScheme:{">":"pink","<":"lightblue"}}]}}});function GV(e){return e.split(">").filter(t=>/\S/.test(t)).map(t=>{let[r,...n]=t.split(`
53
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xe.default.createElement(yt.DialogContent,{className:i.dialogContent},v?xe.default.createElement(IM.ErrorMessage,{error:v}):null,xe.default.createElement(Co,{value:a,onChange:w=>u(w.target.value),label:"BLAST blastDatabase",select:!0},_.map(w=>xe.default.createElement(yt.MenuItem,{value:w,key:w},w))),xe.default.createElement(Co,{value:p,onChange:w=>l(w.target.value),label:"MSA Algorithm",select:!0},y.map(w=>xe.default.createElement(yt.MenuItem,{value:w,key:w},w))),xe.default.createElement(Co,{value:s,onChange:w=>c(w.target.value),label:"Choose isoform to BLAST",select:!0},d.map(w=>xe.default.createElement(yt.MenuItem,{value:et(w),key:w.id()},dh(r)," - ",dn(w)))),xe.default.createElement(Co,{variant:"outlined",multiline:!0,minRows:5,maxRows:10,fullWidth:!0,value:h?`>${dn(f)}
57
- ${h}`:"Loading...",InputProps:{readOnly:!0,classes:{input:i.textAreaFont}}}),xe.default.createElement(yt.DialogActions,null,xe.default.createElement(yt.Button,{color:"primary",variant:"contained",onClick:()=>{kM({feature:f,view:o,newViewTitle:`NCBI BLAST - ${dh(r)} - ${dn(f)} - ${p}`}).setBlastParams({blastProgram:"blastp",blastDatabase:a,msaAlgorithm:p,selectedTranscript:f,proteinSequence:h}),t()},disabled:!h},"Submit"),xe.default.createElement(yt.Button,{color:"secondary",variant:"contained",onClick:()=>t()},"Cancel")))}),RM=_U;var LM=RM;var pe=x(R()),o2=x(D()),a2=x(Te()),Ge=x(B()),Hc=x(Le()),u2=x(St());async function FM(){let e=await fetch("https://jbrowse.org/demos/msaview/knownCanonical/list.txt");if(!e.ok)throw new Error(`HTTP ${e.status} fetching list ${await e.text()}`);return(await e.text()).split(`
58
- `).map(r=>r.trim()).filter(r=>!!r)}function xi(e){let t=e.length;for(;--t>=0;)e[t]=0}var bU=0,SO=1,gU=2,yU=3,wU=258,Fh=29,$o=256,No=$o+1+Fh,yi=30,Dh=19,xO=2*No+1,pn=15,hh=16,SU=7,Nh=256,EO=16,MO=17,OO=18,Ph=new Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]),Rc=new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),xU=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),AO=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),EU=512,ar=new Array((No+2)*2);xi(ar);var Lo=new Array(yi*2);xi(Lo);var Bo=new Array(EU);xi(Bo);var zo=new Array(wU-yU+1);xi(zo);var Bh=new Array(Fh);xi(Bh);var Lc=new Array(yi);xi(Lc);function mh(e,t,r,n,i){this.static_tree=e,this.extra_bits=t,this.extra_base=r,this.elems=n,this.max_length=i,this.has_stree=e&&e.length}var PO,qO,kO;function vh(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}var TO=e=>e<256?Bo[e]:Bo[256+(e>>>7)],Ho=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},We=(e,t,r)=>{e.bi_valid>hh-r?(e.bi_buf|=t<<e.bi_valid&65535,Ho(e,e.bi_buf),e.bi_buf=t>>hh-e.bi_valid,e.bi_valid+=r-hh):(e.bi_buf|=t<<e.bi_valid&65535,e.bi_valid+=r)},Dt=(e,t,r)=>{We(e,r[t*2],r[t*2+1])},CO=(e,t)=>{let r=0;do r|=e&1,e>>>=1,r<<=1;while(--t>0);return r>>>1},MU=e=>{e.bi_valid===16?(Ho(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=e.bi_buf&255,e.bi_buf>>=8,e.bi_valid-=8)},OU=(e,t)=>{let r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,p=t.stat_desc.max_length,l,d,s,c,f,m,v=0;for(c=0;c<=pn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<xO;l++)d=e.heap[l],c=r[r[d*2+1]*2+1]+1,c>p&&(c=p,v++),r[d*2+1]=c,!(d>n)&&(e.bl_count[c]++,f=0,d>=u&&(f=a[d-u]),m=r[d*2],e.opt_len+=m*(c+f),o&&(e.static_len+=m*(i[d*2+1]+f)));if(v!==0){do{for(c=p-1;e.bl_count[c]===0;)c--;e.bl_count[c]--,e.bl_count[c+1]+=2,e.bl_count[p]--,v-=2}while(v>0);for(c=p;c!==0;c--)for(d=e.bl_count[c];d!==0;)s=e.heap[--l],!(s>n)&&(r[s*2+1]!==c&&(e.opt_len+=(c-r[s*2+1])*r[s*2],r[s*2+1]=c),d--)}},jO=(e,t,r)=>{let n=new Array(pn+1),i=0,o,a;for(o=1;o<=pn;o++)i=i+r[o-1]<<1,n[o]=i;for(a=0;a<=t;a++){let u=e[a*2+1];u!==0&&(e[a*2]=CO(n[u]++,u))}},AU=()=>{let e,t,r,n,i,o=new Array(pn+1);for(r=0,n=0;n<Fh-1;n++)for(Bh[n]=r,e=0;e<1<<Ph[n];e++)zo[r++]=n;for(zo[r-1]=n,i=0,n=0;n<16;n++)for(Lc[n]=i,e=0;e<1<<Rc[n];e++)Bo[i++]=n;for(i>>=7;n<yi;n++)for(Lc[n]=i<<7,e=0;e<1<<Rc[n]-7;e++)Bo[256+i++]=n;for(t=0;t<=pn;t++)o[t]=0;for(e=0;e<=143;)ar[e*2+1]=8,e++,o[8]++;for(;e<=255;)ar[e*2+1]=9,e++,o[9]++;for(;e<=279;)ar[e*2+1]=7,e++,o[7]++;for(;e<=287;)ar[e*2+1]=8,e++,o[8]++;for(jO(ar,No+1,o),e=0;e<yi;e++)Lo[e*2+1]=5,Lo[e*2]=CO(e,5);PO=new mh(ar,Ph,$o+1,No,pn),qO=new mh(Lo,Rc,0,yi,pn),kO=new mh(new Array(0),xU,0,Dh,SU)},IO=e=>{let t;for(t=0;t<No;t++)e.dyn_ltree[t*2]=0;for(t=0;t<yi;t++)e.dyn_dtree[t*2]=0;for(t=0;t<Dh;t++)e.bl_tree[t*2]=0;e.dyn_ltree[Nh*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},RO=e=>{e.bi_valid>8?Ho(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},DM=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},_h=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&DM(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!DM(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},NM=(e,t,r)=>{let n,i,o=0,a,u;if(e.sym_next!==0)do n=e.pending_buf[e.sym_buf+o++]&255,n+=(e.pending_buf[e.sym_buf+o++]&255)<<8,i=e.pending_buf[e.sym_buf+o++],n===0?Dt(e,i,t):(a=zo[i],Dt(e,a+$o+1,t),u=Ph[a],u!==0&&(i-=Bh[a],We(e,i,u)),n--,a=TO(n),Dt(e,a,r),u=Rc[a],u!==0&&(n-=Lc[a],We(e,n,u)));while(o<e.sym_next);Dt(e,Nh,t)},qh=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,p=-1,l;for(e.heap_len=0,e.heap_max=xO,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=p=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=p<2?++p:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=p,a=e.heap_len>>1;a>=1;a--)_h(e,r,a);l=o;do 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i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=kU(e)),qh(e,e.l_desc),qh(e,e.d_desc),a=PU(e),i=e.opt_len+3+7>>>3,o=e.static_len+3+7>>>3,o<=i&&(i=o)):i=o=r+5,r+4<=i&&t!==-1?LO(e,t,r,n):e.strategy===4||o===i?(We(e,(SO<<1)+(n?1:0),3),NM(e,ar,Lo)):(We(e,(gU<<1)+(n?1:0),3),qU(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),NM(e,e.dyn_ltree,e.dyn_dtree)),IO(e),n&&RO(e)},IU=(e,t,r)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=r,t===0?e.dyn_ltree[r*2]++:(e.matches++,t--,e.dyn_ltree[(zo[r]+$o+1)*2]++,e.dyn_dtree[TO(t)*2]++),e.sym_next===e.sym_end),RU=TU,LU=LO,FU=jU,DU=IU,NU=CU,BU={_tr_init:RU,_tr_stored_block:LU,_tr_flush_block:FU,_tr_tally:DU,_tr_align:NU},zU=(e,t,r,n)=>{let i=e&65535|0,o=e>>>16&65535|0,a=0;for(;r!==0;){a=r>2e3?2e3:r,r-=a;do i=i+t[n++]|0,o=o+i|0;while(--a);i%=65521,o%=65521}return i|o<<16|0},Vo=zU,HU=()=>{let e,t=[];for(var r=0;r<256;r++){e=r;for(var 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t=e.length;for(;--t>=0;)e[t]=0},hW=e=>{let t,r,n,i=e.w_size;t=e.hash_size,n=t;do r=e.head[--n],e.head[n]=r>=i?r-i:0;while(--t);t=i,n=t;do r=e.prev[--n],e.prev[n]=r>=i?r-i:0;while(--t)},mW=(e,t,r)=>(t<<e.hash_shift^r)&e.hash_mask,zr=mW,tt=e=>{let t=e.state,r=t.pending;r>e.avail_out&&(r=e.avail_out),r!==0&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+r),e.next_out),e.next_out+=r,t.pending_out+=r,e.total_out+=r,e.avail_out-=r,t.pending-=r,t.pending===0&&(t.pending_out=0))},rt=(e,t)=>{GU(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,tt(e.strm)},Y=(e,t)=>{e.pending_buf[e.pending++]=t},jo=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=t&255},Lh=(e,t,r,n)=>{let i=e.avail_in;return i>n&&(i=n),i===0?0:(e.avail_in-=i,t.set(e.input.subarray(e.next_in,e.next_in+i),r),e.state.wrap===1?e.adler=Vo(e.adler,t,i,r):e.state.wrap===2&&(e.adler=ge(e.adler,t,i,r)),e.next_in+=i,e.total_in+=i,i)},FO=(e,t)=>{let r=e.max_chain_length,n=e.strstart,i,o,a=e.prev_length,u=e.nice_match,p=e.strstart>e.w_size-Bt?e.strstart-(e.w_size-Bt):0,l=e.window,d=e.w_mask,s=e.prev,c=e.strstart+Dr,f=l[n+a-1],m=l[n+a];e.prev_length>=e.good_match&&(r>>=2),u>e.lookahead&&(u=e.lookahead);do if(i=t,!(l[i+a]!==m||l[i+a-1]!==f||l[i]!==l[n]||l[++i]!==l[n+1])){n+=2,i++;do;while(l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&n<c);if(o=Dr-(c-n),n=c-Dr,o>a){if(e.match_start=t,a=o,o>=u)break;f=l[n+a-1],m=l[n+a]}}while((t=s[t&d])>p&&--r!==0);return a<=e.lookahead?a:e.lookahead},Si=e=>{let t=e.w_size,r,n,i;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-Bt)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),hW(e),n+=t),e.strm.avail_in===0)break;if(r=Lh(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=V)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=zr(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=zr(e,e.ins_h,e.window[i+V-1]),e.prev[i&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=i,i++,e.insert--,!(e.lookahead+e.insert<V)););}while(e.lookahead<Bt&&e.strm.avail_in!==0)},DO=(e,t)=>{let r=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,n,i,o,a=0,u=e.strm.avail_in;do{if(n=65535,o=e.bi_valid+42>>3,e.strm.avail_out<o||(o=e.strm.avail_out-o,i=e.strstart-e.block_start,n>i+e.strm.avail_in&&(n=i+e.strm.avail_in),n>o&&(n=o),n<r&&(n===0&&t!==lt||t===Br||n!==i+e.strm.avail_in)))break;a=t===lt&&n===i+e.strm.avail_in?1:0,kh(e,0,0,a),e.pending_buf[e.pending-4]=n,e.pending_buf[e.pending-3]=n>>8,e.pending_buf[e.pending-2]=~n,e.pending_buf[e.pending-1]=~n>>8,tt(e.strm),i&&(i>n&&(i=n),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+i),e.strm.next_out),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i,e.block_start+=i,n-=i),n&&(Lh(e.strm,e.strm.output,e.strm.next_out,n),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n)}while(a===0);return u-=e.strm.avail_in,u&&(u>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=u&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-u,e.strm.next_in),e.strstart),e.strstart+=u,e.insert+=u>e.w_size-e.insert?e.w_size-e.insert:u),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),a?Oi:t!==Br&&t!==lt&&e.strm.avail_in===0&&e.strstart===e.block_start?Mi:(o=e.window_size-e.strstart,e.strm.avail_in>o&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,o+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),o>e.strm.avail_in&&(o=e.strm.avail_in),o&&(Lh(e.strm,e.window,e.strstart,o),e.strstart+=o,e.insert+=o>e.w_size-e.insert?e.w_size-e.insert:o),e.high_water<e.strstart&&(e.high_water=e.strstart),o=e.bi_valid+42>>3,o=e.pending_buf_size-o>65535?65535:e.pending_buf_size-o,r=o>e.w_size?e.w_size:o,i=e.strstart-e.block_start,(i>=r||(i||t===lt)&&t!==Br&&e.strm.avail_in===0&&i<=o)&&(n=i>o?o:i,a=t===lt&&e.strm.avail_in===0&&n===i?1:0,kh(e,e.block_start,n,a),e.block_start+=n,tt(e.strm)),a?_n:Ie)},gh=(e,t)=>{let r,n;for(;;){if(e.lookahead<Bt){if(Si(e),e.lookahead<Bt&&t===Br)return Ie;if(e.lookahead===0)break}if(r=0,e.lookahead>=V&&(e.ins_h=zr(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),r!==0&&e.strstart-r<=e.w_size-Bt&&(e.match_length=FO(e,r)),e.match_length>=V)if(n=Nr(e,e.strstart-e.match_start,e.match_length-V),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=V){e.match_length--;do e.strstart++,e.ins_h=zr(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart;while(--e.match_length!==0);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=zr(e,e.ins_h,e.window[e.strstart+1]);else n=Nr(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(rt(e,!1),e.strm.avail_out===0))return Ie}return e.insert=e.strstart<V-1?e.strstart:V-1,t===lt?(rt(e,!0),e.strm.avail_out===0?_n:Oi):e.sym_next&&(rt(e,!1),e.strm.avail_out===0)?Ie:Mi},bi=(e,t)=>{let r,n,i;for(;;){if(e.lookahead<Bt){if(Si(e),e.lookahead<Bt&&t===Br)return 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if(e.match_available){if(n=Nr(e,0,e.window[e.strstart-1]),n&&rt(e,!1),e.strstart++,e.lookahead--,e.strm.avail_out===0)return Ie}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Nr(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<V-1?e.strstart:V-1,t===lt?(rt(e,!0),e.strm.avail_out===0?_n:Oi):e.sym_next&&(rt(e,!1),e.strm.avail_out===0)?Ie:Mi},vW=(e,t)=>{let r,n,i,o,a=e.window;for(;;){if(e.lookahead<=Dr){if(Si(e),e.lookahead<=Dr&&t===Br)return 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e.insert=0,t===lt?(rt(e,!0),e.strm.avail_out===0?_n:Oi):e.sym_next&&(rt(e,!1),e.strm.avail_out===0)?Ie:Mi};function Ft(e,t,r,n,i){this.good_length=e,this.max_lazy=t,this.nice_length=r,this.max_chain=n,this.func=i}var Ro=[new Ft(0,0,0,0,DO),new Ft(4,4,8,4,gh),new Ft(4,5,16,8,gh),new Ft(4,6,32,32,gh),new Ft(4,4,16,16,bi),new Ft(8,16,32,32,bi),new Ft(8,16,128,128,bi),new Ft(8,32,128,256,bi),new Ft(32,128,258,1024,bi),new Ft(32,258,258,4096,bi)],bW=e=>{e.window_size=2*e.w_size,Fr(e.head),e.max_lazy_match=Ro[e.level].max_lazy,e.good_match=Ro[e.level].good_length,e.nice_match=Ro[e.level].nice_length,e.max_chain_length=Ro[e.level].max_chain,e.strstart=0,e.block_start=0,e.lookahead=0,e.insert=0,e.match_length=e.prev_length=V-1,e.match_available=0,e.ins_h=0};function 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i=Nc+(r.w_bits-8<<4)<<8,o=-1;if(r.strategy>=kc||r.level<2?o=0:r.level<6?o=1:r.level===6?o=2:o=3,i|=o<<6,r.strstart!==0&&(i|=dW),i+=31-i%31,jo(r,i),r.strstart!==0&&(jo(r,e.adler>>>16),jo(r,e.adler&65535)),e.adler=1,r.status=hn,tt(e),r.pending!==0)return r.last_flush=-1,Ee}if(r.status===zh){if(e.adler=0,Y(r,31),Y(r,139),Y(r,8),r.gzhead)Y(r,(r.gzhead.text?1:0)+(r.gzhead.hcrc?2:0)+(r.gzhead.extra?4:0)+(r.gzhead.name?8:0)+(r.gzhead.comment?16:0)),Y(r,r.gzhead.time&255),Y(r,r.gzhead.time>>8&255),Y(r,r.gzhead.time>>16&255),Y(r,r.gzhead.time>>24&255),Y(r,r.level===9?2:r.strategy>=kc||r.level<2?4:0),Y(r,r.gzhead.os&255),r.gzhead.extra&&r.gzhead.extra.length&&(Y(r,r.gzhead.extra.length&255),Y(r,r.gzhead.extra.length>>8&255)),r.gzhead.hcrc&&(e.adler=ge(e.adler,r.pending_buf,r.pending,0)),r.gzindex=0,r.status=Ch;else if(Y(r,0),Y(r,0),Y(r,0),Y(r,0),Y(r,0),Y(r,r.level===9?2:r.strategy>=kc||r.level<2?4:0),Y(r,pW),r.status=hn,tt(e),r.pending!==0)return r.last_flush=-1,Ee}if(r.status===Ch){if(r.gzhead.extra){let i=r.pending,o=(r.gzhead.extra.length&65535)-r.gzindex;for(;r.pending+o>r.pending_buf_size;){let u=r.pending_buf_size-r.pending;if(r.pending_buf.set(r.gzhead.extra.subarray(r.gzindex,r.gzindex+u),r.pending),r.pending=r.pending_buf_size,r.gzhead.hcrc&&r.pending>i&&(e.adler=ge(e.adler,r.pending_buf,r.pending-i,i)),r.gzindex+=u,tt(e),r.pending!==0)return r.last_flush=-1,Ee;i=0,o-=u}let a=new Uint8Array(r.gzhead.extra);r.pending_buf.set(a.subarray(r.gzindex,r.gzindex+o),r.pending),r.pending+=o,r.gzhead.hcrc&&r.pending>i&&(e.adler=ge(e.adler,r.pending_buf,r.pending-i,i)),r.gzindex=0}r.status=jh}if(r.status===jh){if(r.gzhead.name){let i=r.pending,o;do{if(r.pending===r.pending_buf_size){if(r.gzhead.hcrc&&r.pending>i&&(e.adler=ge(e.adler,r.pending_buf,r.pending-i,i)),tt(e),r.pending!==0)return 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e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.time=l),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,O[2]=l>>>16&255,O[3]=l>>>24&255,r.check=ge(r.check,O,4,0)),l=0,d=0,r.mode=eO;case eO:for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.xflags=l&255,r.head.os=l>>8),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,r.check=ge(r.check,O,2,0)),l=0,d=0,r.mode=tO;case tO:if(r.flags&1024){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.length=l,r.head&&(r.head.extra_len=l),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,r.check=ge(r.check,O,2,0)),l=0,d=0}else r.head&&(r.head.extra=null);r.mode=rO;case rO:if(r.flags&1024&&(f=r.length,f>u&&(f=u),f&&(r.head&&(A=r.head.extra_len-r.length,r.head.extra||(r.head.extra=new Uint8Array(r.head.extra_len)),r.head.extra.set(n.subarray(o,o+f),A)),r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,r.length-=f),r.length))break e;r.length=0,r.mode=nO;case nO:if(r.flags&2048){if(u===0)break e;f=0;do A=n[o+f++],r.head&&A&&r.length<65536&&(r.head.name+=String.fromCharCode(A));while(A&&f<u);if(r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,A)break e}else r.head&&(r.head.name=null);r.length=0,r.mode=iO;case iO:if(r.flags&4096){if(u===0)break e;f=0;do A=n[o+f++],r.head&&A&&r.length<65536&&(r.head.comment+=String.fromCharCode(A));while(A&&f<u);if(r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,A)break e}else r.head&&(r.head.comment=null);r.mode=oO;case oO:if(r.flags&512){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.wrap&4&&l!==(r.check&65535)){e.msg="header crc mismatch",r.mode=ne;break}l=0,d=0}r.head&&(r.head.hcrc=r.flags>>9&1,r.head.done=!0),e.adler=r.check=0,r.mode=or;break;case aO:for(;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}e.adler=r.check=gO(l),l=0,d=0,r.mode=Dc;case Dc:if(r.havedict===0)return e.next_out=a,e.avail_out=p,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,hG;e.adler=r.check=1,r.mode=or;case or:if(t===dG||t===Cc)break e;case wh:if(r.last){l>>>=d&7,d-=d&7,r.mode=xh;break}for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}switch(r.last=l&1,l>>>=1,d-=1,l&3){case 0:r.mode=uO;break;case 1:if(SG(r),r.mode=jc,t===Cc){l>>>=2,d-=2;break e}break;case 2:r.mode=lO;break;case 3:e.msg="invalid block type",r.mode=ne}l>>>=2,d-=2;break;case uO:for(l>>>=d&7,d-=d&7;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if((l&65535)!==(l>>>16^65535)){e.msg="invalid stored block lengths",r.mode=ne;break}if(r.length=l&65535,l=0,d=0,r.mode=Sh,t===Cc)break e;case Sh:r.mode=sO;case sO:if(f=r.length,f){if(f>u&&(f=u),f>p&&(f=p),f===0)break e;i.set(n.subarray(o,o+f),a),u-=f,o+=f,p-=f,a+=f,r.length-=f;break}r.mode=or;break;case lO:for(;d<14;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.nlen=(l&31)+257,l>>>=5,d-=5,r.ndist=(l&31)+1,l>>>=5,d-=5,r.ncode=(l&15)+4,l>>>=4,d-=4,r.nlen>286||r.ndist>30){e.msg="too many length or distance symbols",r.mode=ne;break}r.have=0,r.mode=cO;case cO:for(;r.have<r.ncode;){for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.lens[I[r.have++]]=l&7,l>>>=3,d-=3}for(;r.have<19;)r.lens[I[r.have++]]=0;if(r.lencode=r.lendyn,r.lenbits=7,P={bits:r.lenbits},q=Do(fG,r.lens,0,19,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid code lengths set",r.mode=ne;break}r.have=0,r.mode=fO;case fO:for(;r.have<r.nlen+r.ndist;){for(;h=r.lencode[l&(1<<r.lenbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(w<16)l>>>=_,d-=_,r.lens[r.have++]=w;else{if(w===16){for(k=_+2;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(l>>>=_,d-=_,r.have===0){e.msg="invalid bit length repeat",r.mode=ne;break}A=r.lens[r.have-1],f=3+(l&3),l>>>=2,d-=2}else if(w===17){for(k=_+3;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,f=3+(l&7),l>>>=3,d-=3}else{for(k=_+7;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,f=11+(l&127),l>>>=7,d-=7}if(r.have+f>r.nlen+r.ndist){e.msg="invalid bit length repeat",r.mode=ne;break}for(;f--;)r.lens[r.have++]=A}}if(r.mode===ne)break;if(r.lens[256]===0){e.msg="invalid code -- missing end-of-block",r.mode=ne;break}if(r.lenbits=9,P={bits:r.lenbits},q=Do(WO,r.lens,0,r.nlen,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid literal/lengths set",r.mode=ne;break}if(r.distbits=6,r.distcode=r.distdyn,P={bits:r.distbits},q=Do(GO,r.lens,r.nlen,r.ndist,r.distcode,0,r.work,P),r.distbits=P.bits,q){e.msg="invalid distances set",r.mode=ne;break}if(r.mode=jc,t===Cc)break e;case jc:r.mode=Ic;case Ic:if(u>=6&&p>=258){e.next_out=a,e.avail_out=p,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,oG(e,c),a=e.next_out,i=e.output,p=e.avail_out,o=e.next_in,n=e.input,u=e.avail_in,l=r.hold,d=r.bits,r.mode===or&&(r.back=-1);break}for(r.back=0;h=r.lencode[l&(1<<r.lenbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(y&&!(y&240)){for(S=_,E=y,M=w;h=r.lencode[M+((l&(1<<S+E)-1)>>S)],_=h>>>24,y=h>>>16&255,w=h&65535,!(S+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=S,d-=S,r.back+=S}if(l>>>=_,d-=_,r.back+=_,r.length=w,y===0){r.mode=vO;break}if(y&32){r.back=-1,r.mode=or;break}if(y&64){e.msg="invalid literal/length code",r.mode=ne;break}r.extra=y&15,r.mode=dO;case dO:if(r.extra){for(k=r.extra;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.length+=l&(1<<r.extra)-1,l>>>=r.extra,d-=r.extra,r.back+=r.extra}r.was=r.length,r.mode=pO;case pO:for(;h=r.distcode[l&(1<<r.distbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(!(y&240)){for(S=_,E=y,M=w;h=r.distcode[M+((l&(1<<S+E)-1)>>S)],_=h>>>24,y=h>>>16&255,w=h&65535,!(S+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=S,d-=S,r.back+=S}if(l>>>=_,d-=_,r.back+=_,y&64){e.msg="invalid distance code",r.mode=ne;break}r.offset=w,r.extra=y&15,r.mode=hO;case hO:if(r.extra){for(k=r.extra;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.offset+=l&(1<<r.extra)-1,l>>>=r.extra,d-=r.extra,r.back+=r.extra}if(r.offset>r.dmax){e.msg="invalid distance too far back",r.mode=ne;break}r.mode=mO;case mO:if(p===0)break e;if(f=c-p,r.offset>f){if(f=r.offset-f,f>r.whave&&r.sane){e.msg="invalid distance too far back",r.mode=ne;break}f>r.wnext?(f-=r.wnext,m=r.wsize-f):m=r.wnext-f,f>r.length&&(f=r.length),v=r.window}else v=i,m=a-r.offset,f=r.length;f>p&&(f=p),p-=f,r.length-=f;do i[a++]=v[m++];while(--f);r.length===0&&(r.mode=Ic);break;case vO:if(p===0)break e;i[a++]=r.length,p--,r.mode=Ic;break;case xh:if(r.wrap){for(;d<32;){if(u===0)break e;u--,l|=n[o++]<<d,d+=8}if(c-=p,e.total_out+=c,r.total+=c,r.wrap&4&&c&&(e.adler=r.check=r.flags?ge(r.check,i,c,a-c):Vo(r.check,i,c,a-c)),c=p,r.wrap&4&&(r.flags?l:gO(l))!==r.check){e.msg="incorrect data check",r.mode=ne;break}l=0,d=0}r.mode=_O;case _O:if(r.wrap&&r.flags){for(;d<32;){if(u===0)break 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Uint8Array(e):r.input=e,r.next_in=0,r.avail_in=r.input.length;;){for(r.avail_out===0&&(r.output=new Uint8Array(n),r.next_out=0,r.avail_out=n),o=ur.inflate(r,a),o===Ah&&i&&(o=ur.inflateSetDictionary(r,i),o===Go?o=ur.inflate(r,a):o===wO&&(o=Ah));r.avail_in>0&&o===Oh&&r.state.wrap>0&&e[r.next_in]!==0;)ur.inflateReset(r),o=ur.inflate(r,a);switch(o){case zG:case wO:case Ah:case HG:return this.onEnd(o),this.ended=!0,!1}if(u=r.avail_out,r.next_out&&(r.avail_out===0||o===Oh))if(this.options.to==="string"){let p=Wo.utf8border(r.output,r.next_out),l=r.next_out-p,d=Wo.buf2string(r.output,p);r.next_out=l,r.avail_out=n-l,l&&r.output.set(r.output.subarray(p,p+l),0),this.onData(d)}else this.onData(r.output.length===r.next_out?r.output:r.output.subarray(0,r.next_out));if(!(o===Go&&u===0)){if(o===Oh)return o=ur.inflateEnd(this.strm),this.onEnd(o),this.ended=!0,!0;if(r.avail_in===0)break}}return!0};Zo.prototype.onData=function(e){this.chunks.push(e)};Zo.prototype.onEnd=function(e){e===Go&&(this.options.to==="string"?this.result=this.chunks.join(""):this.result=Bc.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};function Vh(e,t){let r=new Zo(t);if(r.push(e),r.err)throw r.msg||vn[r.err];return r.result}function VG(e,t){return t=t||{},t.raw=!0,Vh(e,t)}var UG=Zo,WG=Vh,GG=VG,$G=Vh,YG=Ei,XG={Inflate:UG,inflate:WG,inflateRaw:GG,ungzip:$G,constants:YG},{Deflate:Tne,deflate:Cne,deflateRaw:jne,gzip:Ine}=nG,{Inflate:Rne,inflate:Lne,inflateRaw:Fne,ungzip:ZG}=XG;var n2=ZG;async function KG(e){let t=await fetch(e);if(!t.ok)throw new Error(`HTTP ${t.status} fetching ${await t.text()}`);let r=await t.arrayBuffer();return new TextDecoder().decode(n2(r))}async function i2({userSelection:e,session:t,newViewTitle:r,view:n,feature:i}){let o=await KG(`https://jbrowse.org/demos/msaview/knownCanonical/${e}.mfa.gz`);t.addView("MsaView",{type:"MsaView",displayName:r,treeAreaWidth:200,treeWidth:100,drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",treeFilehandle:{uri:"https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh"},treeMetadataFilehandle:{uri:"https://s3.amazonaws.com/jbrowse.org/demos/app/species.json"},data:{msa:o},connectedViewId:n.id,connectedFeature:i.toJSON()})}var JG=(0,u2.makeStyles)()({dialogContent:{width:"80em"}}),QG=(0,o2.observer)(function({model:t,feature:r,handleClose:n}){let i=(0,Hc.getSession)(t),o=(0,Hc.getContainingView)(t),{classes:a}=JG(),[u,p]=(0,pe.useState)(),[l,d]=(0,pe.useState)();(0,pe.useEffect)(()=>{(async()=>{try{let h=await FM();d(h);let _=new Set(h),w=ko(r).find(S=>_.has(et(S)));w&&v(et(w))}catch(h){console.error(h),p(h)}})()},[r]);let s=new Set(l),c=ko(r),f=c.find(h=>s.has(et(h))),[m,v]=(0,pe.useState)(et(c[0]));return pe.default.createElement(pe.default.Fragment,null,pe.default.createElement(Ge.DialogContent,{className:a.dialogContent},pe.default.createElement(Ge.Typography,null,"The source data for these multiple sequence alignments is from"," ",pe.default.createElement("a",{href:"https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/"},"knownCanonical.multiz100way.protAA.fa.gz")),u?pe.default.createElement(a2.ErrorMessage,{error:u}):null,l&&!f?pe.default.createElement("div",{style:{color:"red"}},"No MSA data for this gene found"):null,pe.default.createElement(Ge.TextField,{value:m,onChange:h=>v(h.target.value),label:"Choose isoform to view MSA for",select:!0},c.filter(h=>s.has(et(h))).map(h=>pe.default.createElement(Ge.MenuItem,{value:et(h),key:h.id()},dn(h)," (has data)")),c.filter(h=>!s.has(et(h))).map(h=>pe.default.createElement(Ge.MenuItem,{value:et(h),key:h.id(),disabled:!0},dn(h))))),pe.default.createElement(Ge.DialogActions,null,pe.default.createElement(Ge.Button,{color:"primary",variant:"contained",onClick:()=>{(async()=>{try{if(!f)return;await i2({userSelection:m,session:i,newViewTitle:"",view:o,feature:f}),n()}catch(h){console.error(h),p(h)}})()}},"Submit"),pe.default.createElement(Ge.Button,{color:"secondary",variant:"contained",onClick:()=>n()},"Cancel")))}),s2=QG;function Uh({handleClose:e,feature:t,model:r}){let[n,i]=(0,ft.useState)(0);return ft.default.createElement(l2.Dialog,{maxWidth:"xl",title:"Launch MSA view",onClose:()=>e(),open:!0},ft.default.createElement(yn.Box,{sx:{borderBottom:1,borderColor:"divider"}},ft.default.createElement(yn.Tabs,{value:n,onChange:(o,a)=>i(a)},ft.default.createElement(yn.Tab,{label:"NCBI BLAST query",...fh(0)}),ft.default.createElement(yn.Tab,{label:"UCSC 100-way dataset",...fh(1)}))),ft.default.createElement(ch,{value:n,index:0},ft.default.createElement(LM,{handleClose:e,feature:t,model:r})),ft.default.createElement(ch,{value:n,index:1},ft.default.createElement(s2,{model:r,feature:t,handleClose:e})))}function e$(e){return e.name==="LinearBasicDisplay"}function t$(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,i=(0,Vc.getContainingTrack)(t);return[...r(),...n?[{label:"Launch MSA view",icon:c2.default,onClick:()=>{(0,Vc.getSession)(i).queueDialog(a=>[Uh,{model:i,handleClose:a,feature:n}])}}]:[]]}}})}function Wh(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(e$(t)&&(t.stateModel=t$(t.stateModel)),t))}var b2=x(R());var Ko=x(R()),v2=x(D());var Wc=x(R()),d2=x(D()),p2=x(Le());var f2=x(St()),Uc=(0,f2.makeStyles)()({highlight:{height:"100%",background:"rgba(255,255,0,0.2)",border:"1px solid rgba(50,50,0,0.2)",position:"absolute",zIndex:1e3,textAlign:"center",pointerEvents:"none",overflow:"hidden"}});function r$(e,t){return e.getCanonicalRefName(t)??t}var n$=(0,d2.observer)(function({model:t}){let{classes:r}=Uc(),{assemblyManager:n,views:i}=(0,p2.getSession)(t),o=i.find(u=>u.type==="MsaView"),a=n.get(t.assemblyNames[0]);return a?Wc.default.createElement(Wc.default.Fragment,null,o?.connectedHighlights.map((u,p)=>{let l=r$(a,u.refName),d=t.bpToPx({refName:l,coord:u.start}),s=t.bpToPx({refName:l,coord:u.end});if(d&&s){let c=Math.max(Math.abs(s.offsetPx-d.offsetPx),4),f=Math.min(d.offsetPx,s.offsetPx)-t.offsetPx;return Wc.default.createElement("div",{key:`${JSON.stringify(u)}-${p}`,className:r.highlight,style:{left:f,width:c}})}return null})):null}),h2=n$;var Gh=x(R()),$h=x(D()),Yh=x(Le());var i$=(0,$h.observer)(function({model:t}){let{hovered:r}=(0,Yh.getSession)(t);return r&&typeof r=="object"&&"hoverPosition"in r?Gh.default.createElement(o$,{model:t}):null}),o$=(0,$h.observer)(function({model:t}){let{classes:r}=Uc(),n=(0,Yh.getSession)(t);if(n.views.some(i=>i.type==="MsaView")){let{hovered:i}=n,{offsetPx:o}=t,{coord:a,refName:u}=i.hoverPosition,p=t.bpToPx({refName:u,coord:a-1}),l=t.bpToPx({refName:u,coord:a});if(p&&l){let d=Math.max(Math.abs(l.offsetPx-p.offsetPx),4),s=Math.min(p.offsetPx,l.offsetPx)-o;return Gh.default.createElement("div",{className:r.highlight,style:{left:s,width:d}})}}return null}),m2=i$;var a$=(0,v2.observer)(function({model:t}){return Ko.default.createElement(Ko.default.Fragment,null,Ko.default.createElement(h2,{model:t}),Ko.default.createElement(m2,{model:t}))}),_2=a$;function Xh(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t=[],{model:r})=>[...t,b2.default.createElement(_2,{key:"highlight_protein_viewer_msaview",model:r})])}var Gc=class extends g2.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=im}install(r){sh(r),Wh(r),Xh(r)}configure(r){(0,y2.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:w2.default,onClick:n=>{n.addView("MsaView",{})}})}};return A2(u$);})();
56
+ `);return await nO({algorithm:n,sequence:u,onProgress:l=>e.setProgress(l)})}var lO=x(Se());function sO(e){return!!e&&typeof e=="object"&&"hoverFeature"in e&&"hoverPosition"in e}function cO({model:e}){let{hovered:t}=(0,lO.getSession)(e),{transcriptToMsaMap:r,connectedView:n}=e;if(n?.initialized&&r&&sO(t)){let{coord:i}=t.hoverPosition,{g2p:o}=r,a=o[i];if(a!==void 0)return e.seqCoordToRowSpecificGlobalCoord("QUERY",a+1)}}function Ac({model:e,coord:t}){let{transcriptToMsaMap:r}=e;if(t===void 0||r===void 0)return;let n=t-1,i=e.globalCoordToRowSpecificSeqCoord("QUERY",n)||0,o=e.globalCoordToRowSpecificSeqCoord("QUERY",n+1)||0,{refName:a,p2g:u}=r,f=u[i],l=u[o];return f!==void 0&&l!==void 0?{refName:a,start:Math.min(f,l),end:Math.max(f,l)}:void 0}var pO=x(fO());function ch(){return _e.types.compose(dO.BaseViewModel,ah(),_e.types.model("MsaView",{connectedViewId:_e.types.maybe(_e.types.string),connectedFeature:_e.types.frozen(),connectedHighlights:_e.types.array(_e.types.model({refName:_e.types.string,start:_e.types.number,end:_e.types.number})),blastParams:_e.types.frozen(),zoomToBaseLevel:!1})).volatile(()=>({rid:void 0,progress:"",error:void 0})).views(e=>({ungappedCoordMap(t,r){let i=e.rows.find(o=>o[0]===t)?.[1];if(i&&r<i.length){let o=0,a=0;for(;a<r;a++,o++)for(;i[o]==="-";)o++;return o}}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?(0,pO.genomeToTranscriptSeqMapping)(e.connectedFeature):void 0}})).views(e=>({get mouseCol2(){return cO({model:e})},get clickCol2(){}})).views(e=>({get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,kc.getSession)(e);return t.find(r=>r.id===e.connectedViewId)}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,_e.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,_e.cast)([])},setBlastParams(t){e.blastParams=t}})).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>e.setZoomToBaseLevel(!e.zoomToBaseLevel)}]},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,kc.getSession)(e);return t.find(r=>r.id===e.connectedViewId)}})).actions(e=>({afterCreate(){(0,_e.addDisposer)(e,(0,qc.autorun)(async()=>{if(e.blastParams)try{e.setProgress("Submitting query");let t=await uO({self:e});e.setData(t),e.setBlastParams(void 0),e.setProgress("")}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})),(0,_e.addDisposer)(e,(0,qc.autorun)(()=>{let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:Ac({model:e,coord:t}),i=r===void 0?void 0:Ac({model:e,coord:r});e.setConnectedHighlights([n,i].filter(o=>!!o))})),(0,_e.addDisposer)(e,(0,qc.autorun)(()=>{let{connectedView:t,zoomToBaseLevel:r,mouseClickCol:n}=e,{assemblyManager:i}=(0,kc.getSession)(e),o=n===void 0?void 0:Ac({model:e,coord:n});if(!(!o||!t))if(r)t.navTo(o);else{let a=i.get(t.assemblyNames[0])?.getCanonicalRefName(o.refName)??o.refName;t.centerAt(o.start,a)}}))}}))}var pU=(0,OO.lazy)(()=>Promise.resolve().then(()=>(EO(),xO)));function hh(e){e.addViewType(()=>new MO.default({name:"MsaView",stateModel:ch(),ReactComponent:pU}))}var Zc=x(Se()),_2=x(AO());var ht=x(I()),v2=x(qe()),wn=x(N());var mh=x(I()),PO=x(N());function vh(e){let{children:t,value:r,index:n,...i}=e;return mh.default.createElement("div",{role:"tabpanel",hidden:r!==n,id:`gtabpanel-${n}`,"aria-labelledby":`gtab-${n}`,...i},r===n&&mh.default.createElement(PO.Box,{sx:{p:3}},t))}function _h(e){return{id:`gtab-${e}`,"aria-controls":`gtabpanel-${e}`}}var Ae=x(I()),BO=x(D()),Et=x(N()),zO=x(Mt()),HO=x(Se()),VO=x(qe());function Co(e){let t=e.get("subfeatures")??[];return t.some(r=>r.get("type")==="CDS")?[e]:t.filter(r=>r.get("subfeatures")?.some(n=>n.get("type")==="CDS"))}function nt(e){return e===void 0?"":e.get("name")||e.get("id")}function pn(e){return e===void 0?"":[e.get("name"),e.get("id")].filter(t=>!!t).join(" ")}function jo(e){return e===void 0?"":[e.get("gene_name")||e.get("name"),e.get("id")].filter(t=>!!t).join(" ")}var bi=x(Se());function _U(e,t){return e.map(r=>t.slice(r.start,r.end)).join("")}function bU({cds:e,sequence:t,codonTable:r}){let n=_U(e,t),i="";for(let o=0;o<n.length;o+=3)i+=r[n.slice(o,o+3)]||"&";return i}function gU(e,t){return e.map(r=>({...r,start:t-r.end,end:t-r.start})).sort((r,n)=>r.start-n.start)}function qO(e){return`${e.start}-${e.end}`}function yU(e){return e.filter((t,r,n)=>!r||qO(t)!==qO(n[r-1]))}function kO({selectedTranscript:e,seq:t}){let r=e.toJSON(),n=yU(r.subfeatures.sort((i,o)=>i.start-o.start).map(i=>({...i,start:i.start-r.start,end:i.end-r.start})).filter(i=>i.type==="CDS"));return bU({cds:r.strand===-1?gU(n,t.length):n,sequence:r.strand===-1?(0,bi.revcom)(t):t,codonTable:(0,bi.generateCodonTable)(bi.defaultCodonTable)})}var Io=x(I()),IO=x(Se()),RO=x(CO()),jO=5e5;function LO({view:e,feature:t,upDownBp:r=0,forceLoad:n=!0}){let[i,o]=(0,Io.useState)(),[a,u]=(0,Io.useState)();return(0,Io.useEffect)(()=>{if(e){let{assemblyManager:f,rpcManager:l}=(0,IO.getSession)(e),[d]=e?.assemblyNames||[];async function s(c,p,m){let v=await f.waitForAssembly(d);if(!v)throw new Error("assembly not found");let h="getSequence",_=await l.call(h,"CoreGetFeatures",{adapterConfig:(0,RO.getConf)(v,["sequence","adapter"]),sessionId:h,regions:[{start:c,end:p,refName:v.getCanonicalRefName(m),assemblyName:d}]}),[y]=_;return y?.get("seq")||""}(async()=>{try{u(void 0),o(void 0);let{start:c,end:p,refName:m}=t.toJSON();if(!n&&p-c>jO)o({error:`Genomic sequence larger than ${jO}bp, use "force load" button to display`});else{let v=c-r,h=p+r,_=await s(c,p,m),y=await s(Math.max(0,v),c,m),w=await s(p,h,m);o({seq:_,upstream:y,downstream:w})}}catch(c){console.error(c),u(c)}})()}},[t,e,r,n]),{sequence:i,error:a}}var bh=x(I()),FO=x(N());function wU({children:e,...t}){return bh.default.createElement("div",null,bh.default.createElement(FO.TextField,{...t},e))}var Ro=wU;var DO=x(Se());function NO({newViewTitle:e,view:t,feature:r}){return(0,DO.getSession)(t).addView("MsaView",{type:"MsaView",displayName:e,connectedViewId:t.id,connectedFeature:r.toJSON(),treeAreaWidth:250,treeWidth:100,drawNodeBubbles:!0,labelsAlignRight:!0,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic"})}var SU=(0,zO.makeStyles)()({dialogContent:{width:"80em"},textAreaFont:{fontFamily:"Courier New"}}),xU=(0,BO.observer)(function({handleClose:t,feature:r,model:n}){let{classes:i}=SU(),o=(0,HO.getContainingView)(n),[a,u]=(0,Ae.useState)("nr"),[f,l]=(0,Ae.useState)("clustalo"),d=Co(r),[s,c]=(0,Ae.useState)(nt(d[0])),p=d.find(w=>nt(w)===s),{sequence:m,error:v}=LO({view:o,feature:p}),h=m&&!("error"in m)?kO({seq:m.seq,selectedTranscript:p}):"",_=["nr","nr_cluster_seq"],y=["clustalo","muscle","kalign","mafft"];return Ae.default.createElement(Et.DialogContent,{className:i.dialogContent},v?Ae.default.createElement(VO.ErrorMessage,{error:v}):null,Ae.default.createElement(Ro,{value:a,onChange:w=>u(w.target.value),label:"BLAST blastDatabase",select:!0},_.map(w=>Ae.default.createElement(Et.MenuItem,{value:w,key:w},w))),Ae.default.createElement(Ro,{value:f,onChange:w=>l(w.target.value),label:"MSA Algorithm",select:!0},y.map(w=>Ae.default.createElement(Et.MenuItem,{value:w,key:w},w))),Ae.default.createElement(Ro,{value:s,onChange:w=>c(w.target.value),label:"Choose isoform to BLAST",select:!0},d.map(w=>Ae.default.createElement(Et.MenuItem,{value:nt(w),key:w.id()},jo(r)," - ",pn(w)))),Ae.default.createElement(Ro,{variant:"outlined",multiline:!0,minRows:5,maxRows:10,fullWidth:!0,value:h?`>${pn(p)}
57
+ ${h}`:"Loading...",InputProps:{readOnly:!0,classes:{input:i.textAreaFont}}}),Ae.default.createElement(Et.DialogActions,null,Ae.default.createElement(Et.Button,{color:"primary",variant:"contained",onClick:()=>{NO({feature:p,view:o,newViewTitle:`NCBI BLAST - ${jo(r)} - ${pn(p)} - ${f}`}).setBlastParams({blastProgram:"blastp",blastDatabase:a,msaAlgorithm:f,selectedTranscript:p,proteinSequence:h}),t()},disabled:!h},"Submit"),Ae.default.createElement(Et.Button,{color:"secondary",variant:"contained",onClick:()=>t()},"Cancel")))}),gh=xU;var me=x(I()),d2=x(D()),p2=x(qe()),Ye=x(N()),Xc=x(Se()),h2=x(Mt());async function UO(){let e=await fetch("https://jbrowse.org/demos/msaview/knownCanonical/list.txt");if(!e.ok)throw new Error(`HTTP ${e.status} fetching list ${await e.text()}`);return(await e.text()).split(`
58
+ `).map(r=>r.trim()).filter(r=>!!r)}function Ei(e){let t=e.length;for(;--t>=0;)e[t]=0}var EU=0,qM=1,OU=2,MU=3,AU=258,Vh=29,Zo=256,Ho=Zo+1+Vh,wi=30,Uh=19,kM=2*Ho+1,hn=15,yh=16,PU=7,Wh=256,TM=16,CM=17,jM=18,Ih=new Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]),Hc=new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),qU=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),IM=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),kU=512,lr=new Array((Ho+2)*2);Ei(lr);var No=new Array(wi*2);Ei(No);var Vo=new Array(kU);Ei(Vo);var Uo=new Array(AU-MU+1);Ei(Uo);var Gh=new Array(Vh);Ei(Gh);var Vc=new Array(wi);Ei(Vc);function wh(e,t,r,n,i){this.static_tree=e,this.extra_bits=t,this.extra_base=r,this.elems=n,this.max_length=i,this.has_stree=e&&e.length}var RM,LM,FM;function Sh(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}var DM=e=>e<256?Vo[e]:Vo[256+(e>>>7)],Wo=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},$e=(e,t,r)=>{e.bi_valid>yh-r?(e.bi_buf|=t<<e.bi_valid&65535,Wo(e,e.bi_buf),e.bi_buf=t>>yh-e.bi_valid,e.bi_valid+=r-yh):(e.bi_buf|=t<<e.bi_valid&65535,e.bi_valid+=r)},zt=(e,t,r)=>{$e(e,r[t*2],r[t*2+1])},NM=(e,t)=>{let r=0;do r|=e&1,e>>>=1,r<<=1;while(--t>0);return r>>>1},TU=e=>{e.bi_valid===16?(Wo(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=e.bi_buf&255,e.bi_buf>>=8,e.bi_valid-=8)},CU=(e,t)=>{let r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,f=t.stat_desc.max_length,l,d,s,c,p,m,v=0;for(c=0;c<=hn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<kM;l++)d=e.heap[l],c=r[r[d*2+1]*2+1]+1,c>f&&(c=f,v++),r[d*2+1]=c,!(d>n)&&(e.bl_count[c]++,p=0,d>=u&&(p=a[d-u]),m=r[d*2],e.opt_len+=m*(c+p),o&&(e.static_len+=m*(i[d*2+1]+p)));if(v!==0){do{for(c=f-1;e.bl_count[c]===0;)c--;e.bl_count[c]--,e.bl_count[c+1]+=2,e.bl_count[f]--,v-=2}while(v>0);for(c=f;c!==0;c--)for(d=e.bl_count[c];d!==0;)s=e.heap[--l],!(s>n)&&(r[s*2+1]!==c&&(e.opt_len+=(c-r[s*2+1])*r[s*2],r[s*2+1]=c),d--)}},BM=(e,t,r)=>{let n=new Array(hn+1),i=0,o,a;for(o=1;o<=hn;o++)i=i+r[o-1]<<1,n[o]=i;for(a=0;a<=t;a++){let u=e[a*2+1];u!==0&&(e[a*2]=NM(n[u]++,u))}},jU=()=>{let e,t,r,n,i,o=new Array(hn+1);for(r=0,n=0;n<Vh-1;n++)for(Gh[n]=r,e=0;e<1<<Ih[n];e++)Uo[r++]=n;for(Uo[r-1]=n,i=0,n=0;n<16;n++)for(Vc[n]=i,e=0;e<1<<Hc[n];e++)Vo[i++]=n;for(i>>=7;n<wi;n++)for(Vc[n]=i<<7,e=0;e<1<<Hc[n]-7;e++)Vo[256+i++]=n;for(t=0;t<=hn;t++)o[t]=0;for(e=0;e<=143;)lr[e*2+1]=8,e++,o[8]++;for(;e<=255;)lr[e*2+1]=9,e++,o[9]++;for(;e<=279;)lr[e*2+1]=7,e++,o[7]++;for(;e<=287;)lr[e*2+1]=8,e++,o[8]++;for(BM(lr,Ho+1,o),e=0;e<wi;e++)No[e*2+1]=5,No[e*2]=NM(e,5);RM=new wh(lr,Ih,Zo+1,Ho,hn),LM=new wh(No,Hc,0,wi,hn),FM=new wh(new Array(0),qU,0,Uh,PU)},zM=e=>{let t;for(t=0;t<Ho;t++)e.dyn_ltree[t*2]=0;for(t=0;t<wi;t++)e.dyn_dtree[t*2]=0;for(t=0;t<Uh;t++)e.bl_tree[t*2]=0;e.dyn_ltree[Wh*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},HM=e=>{e.bi_valid>8?Wo(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},WO=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},xh=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&WO(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!WO(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},GO=(e,t,r)=>{let n,i,o=0,a,u;if(e.sym_next!==0)do n=e.pending_buf[e.sym_buf+o++]&255,n+=(e.pending_buf[e.sym_buf+o++]&255)<<8,i=e.pending_buf[e.sym_buf+o++],n===0?zt(e,i,t):(a=Uo[i],zt(e,a+Zo+1,t),u=Ih[a],u!==0&&(i-=Gh[a],$e(e,i,u)),n--,a=DM(n),zt(e,a,r),u=Hc[a],u!==0&&(n-=Vc[a],$e(e,n,u)));while(o<e.sym_next);zt(e,Wh,t)},Rh=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,f=-1,l;for(e.heap_len=0,e.heap_max=kM,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=f=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=f<2?++f:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=f,a=e.heap_len>>1;a>=1;a--)xh(e,r,a);l=o;do 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o!==0?(o!==i&&(zt(e,o,e.bl_tree),u--),zt(e,TM,e.bl_tree),$e(e,u-3,2)):u<=10?(zt(e,CM,e.bl_tree),$e(e,u-3,3)):(zt(e,jM,e.bl_tree),$e(e,u-11,7));u=0,i=o,a===0?(f=138,l=3):o===a?(f=6,l=3):(f=7,l=4)}},IU=e=>{let t;for($O(e,e.dyn_ltree,e.l_desc.max_code),$O(e,e.dyn_dtree,e.d_desc.max_code),Rh(e,e.bl_desc),t=Uh-1;t>=3&&e.bl_tree[IM[t]*2+1]===0;t--);return e.opt_len+=3*(t+1)+5+5+4,t},RU=(e,t,r,n)=>{let i;for($e(e,t-257,5),$e(e,r-1,5),$e(e,n-4,4),i=0;i<n;i++)$e(e,e.bl_tree[IM[i]*2+1],3);YO(e,e.dyn_ltree,t-1),YO(e,e.dyn_dtree,r-1)},LU=e=>{let t=4093624447,r;for(r=0;r<=31;r++,t>>>=1)if(t&1&&e.dyn_ltree[r*2]!==0)return 0;if(e.dyn_ltree[9*2]!==0||e.dyn_ltree[10*2]!==0||e.dyn_ltree[13*2]!==0)return 1;for(r=32;r<Zo;r++)if(e.dyn_ltree[r*2]!==0)return 1;return 0},XO=!1,FU=e=>{XO||(jU(),XO=!0),e.l_desc=new Sh(e.dyn_ltree,RM),e.d_desc=new Sh(e.dyn_dtree,LM),e.bl_desc=new 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i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=LU(e)),Rh(e,e.l_desc),Rh(e,e.d_desc),a=IU(e),i=e.opt_len+3+7>>>3,o=e.static_len+3+7>>>3,o<=i&&(i=o)):i=o=r+5,r+4<=i&&t!==-1?VM(e,t,r,n):e.strategy===4||o===i?($e(e,(qM<<1)+(n?1:0),3),GO(e,lr,No)):($e(e,(OU<<1)+(n?1:0),3),RU(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),GO(e,e.dyn_ltree,e.dyn_dtree)),zM(e),n&&HM(e)},BU=(e,t,r)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=r,t===0?e.dyn_ltree[r*2]++:(e.matches++,t--,e.dyn_ltree[(Uo[r]+Zo+1)*2]++,e.dyn_dtree[DM(t)*2]++),e.sym_next===e.sym_end),zU=FU,HU=VM,VU=NU,UU=BU,WU=DU,GU={_tr_init:zU,_tr_stored_block:HU,_tr_flush_block:VU,_tr_tally:UU,_tr_align:WU},$U=(e,t,r,n)=>{let i=e&65535|0,o=e>>>16&65535|0,a=0;for(;r!==0;){a=r>2e3?2e3:r,r-=a;do i=i+t[n++]|0,o=o+i|0;while(--a);i%=65521,o%=65521}return i|o<<16|0},Go=$U,YU=()=>{let e,t=[];for(var r=0;r<256;r++){e=r;for(var n=0;n<8;n++)e=e&1?3988292384^e>>>1:e>>>1;t[r]=e}return t},XU=new Uint32Array(YU()),ZU=(e,t,r,n)=>{let i=XU,o=n+r;e^=-1;for(let a=n;a<o;a++)e=e>>>8^i[(e^t[a])&255];return e^-1},we=ZU,_n={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"},Oi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8},{_tr_init:KU,_tr_stored_block:Lh,_tr_flush_block:JU,_tr_tally:Hr,_tr_align:QU}=GU,{Z_NO_FLUSH:Vr,Z_PARTIAL_FLUSH:eW,Z_FULL_FLUSH:tW,Z_FINISH:dt,Z_BLOCK:ZO,Z_OK:Pe,Z_STREAM_END:KO,Z_STREAM_ERROR:Ht,Z_DATA_ERROR:rW,Z_BUF_ERROR:Eh,Z_DEFAULT_COMPRESSION:nW,Z_FILTERED:iW,Z_HUFFMAN_ONLY:Fc,Z_RLE:oW,Z_FIXED:aW,Z_DEFAULT_STRATEGY:uW,Z_UNKNOWN:sW,Z_DEFLATED:Gc}=Oi,lW=9,cW=15,fW=8,dW=29,pW=256,Fh=pW+1+dW,hW=30,mW=19,vW=2*Fh+1,_W=15,V=3,zr=258,Vt=zr+V+1,bW=32,Si=42,$h=57,Dh=69,Nh=73,Bh=91,zh=103,mn=113,Fo=666,De=1,Mi=2,bn=3,Ai=4,gW=3,vn=(e,t)=>(e.msg=_n[t],t),JO=e=>e*2-(e>4?9:0),Br=e=>{let t=e.length;for(;--t>=0;)e[t]=0},yW=e=>{let t,r,n,i=e.w_size;t=e.hash_size,n=t;do r=e.head[--n],e.head[n]=r>=i?r-i:0;while(--t);t=i,n=t;do r=e.prev[--n],e.prev[n]=r>=i?r-i:0;while(--t)},wW=(e,t,r)=>(t<<e.hash_shift^r)&e.hash_mask,Ur=wW,it=e=>{let t=e.state,r=t.pending;r>e.avail_out&&(r=e.avail_out),r!==0&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+r),e.next_out),e.next_out+=r,t.pending_out+=r,e.total_out+=r,e.avail_out-=r,t.pending-=r,t.pending===0&&(t.pending_out=0))},ot=(e,t)=>{JU(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,it(e.strm)},Y=(e,t)=>{e.pending_buf[e.pending++]=t},Lo=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=t&255},Hh=(e,t,r,n)=>{let i=e.avail_in;return i>n&&(i=n),i===0?0:(e.avail_in-=i,t.set(e.input.subarray(e.next_in,e.next_in+i),r),e.state.wrap===1?e.adler=Go(e.adler,t,i,r):e.state.wrap===2&&(e.adler=we(e.adler,t,i,r)),e.next_in+=i,e.total_in+=i,i)},UM=(e,t)=>{let r=e.max_chain_length,n=e.strstart,i,o,a=e.prev_length,u=e.nice_match,f=e.strstart>e.w_size-Vt?e.strstart-(e.w_size-Vt):0,l=e.window,d=e.w_mask,s=e.prev,c=e.strstart+zr,p=l[n+a-1],m=l[n+a];e.prev_length>=e.good_match&&(r>>=2),u>e.lookahead&&(u=e.lookahead);do if(i=t,!(l[i+a]!==m||l[i+a-1]!==p||l[i]!==l[n]||l[++i]!==l[n+1])){n+=2,i++;do;while(l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&n<c);if(o=zr-(c-n),n=c-zr,o>a){if(e.match_start=t,a=o,o>=u)break;p=l[n+a-1],m=l[n+a]}}while((t=s[t&d])>f&&--r!==0);return a<=e.lookahead?a:e.lookahead},xi=e=>{let t=e.w_size,r,n,i;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-Vt)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),yW(e),n+=t),e.strm.avail_in===0)break;if(r=Hh(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=V)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=Ur(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=Ur(e,e.ins_h,e.window[i+V-1]),e.prev[i&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=i,i++,e.insert--,!(e.lookahead+e.insert<V)););}while(e.lookahead<Vt&&e.strm.avail_in!==0)},WM=(e,t)=>{let r=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,n,i,o,a=0,u=e.strm.avail_in;do{if(n=65535,o=e.bi_valid+42>>3,e.strm.avail_out<o||(o=e.strm.avail_out-o,i=e.strstart-e.block_start,n>i+e.strm.avail_in&&(n=i+e.strm.avail_in),n>o&&(n=o),n<r&&(n===0&&t!==dt||t===Vr||n!==i+e.strm.avail_in)))break;a=t===dt&&n===i+e.strm.avail_in?1:0,Lh(e,0,0,a),e.pending_buf[e.pending-4]=n,e.pending_buf[e.pending-3]=n>>8,e.pending_buf[e.pending-2]=~n,e.pending_buf[e.pending-1]=~n>>8,it(e.strm),i&&(i>n&&(i=n),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+i),e.strm.next_out),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i,e.block_start+=i,n-=i),n&&(Hh(e.strm,e.strm.output,e.strm.next_out,n),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n)}while(a===0);return u-=e.strm.avail_in,u&&(u>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=u&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-u,e.strm.next_in),e.strstart),e.strstart+=u,e.insert+=u>e.w_size-e.insert?e.w_size-e.insert:u),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),a?Ai:t!==Vr&&t!==dt&&e.strm.avail_in===0&&e.strstart===e.block_start?Mi:(o=e.window_size-e.strstart,e.strm.avail_in>o&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,o+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),o>e.strm.avail_in&&(o=e.strm.avail_in),o&&(Hh(e.strm,e.window,e.strstart,o),e.strstart+=o,e.insert+=o>e.w_size-e.insert?e.w_size-e.insert:o),e.high_water<e.strstart&&(e.high_water=e.strstart),o=e.bi_valid+42>>3,o=e.pending_buf_size-o>65535?65535:e.pending_buf_size-o,r=o>e.w_size?e.w_size:o,i=e.strstart-e.block_start,(i>=r||(i||t===dt)&&t!==Vr&&e.strm.avail_in===0&&i<=o)&&(n=i>o?o:i,a=t===dt&&e.strm.avail_in===0&&n===i?1:0,Lh(e,e.block_start,n,a),e.block_start+=n,it(e.strm)),a?bn:De)},Oh=(e,t)=>{let r,n;for(;;){if(e.lookahead<Vt){if(xi(e),e.lookahead<Vt&&t===Vr)return De;if(e.lookahead===0)break}if(r=0,e.lookahead>=V&&(e.ins_h=Ur(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),r!==0&&e.strstart-r<=e.w_size-Vt&&(e.match_length=UM(e,r)),e.match_length>=V)if(n=Hr(e,e.strstart-e.match_start,e.match_length-V),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=V){e.match_length--;do e.strstart++,e.ins_h=Ur(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart;while(--e.match_length!==0);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=Ur(e,e.ins_h,e.window[e.strstart+1]);else n=Hr(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(ot(e,!1),e.strm.avail_out===0))return De}return e.insert=e.strstart<V-1?e.strstart:V-1,t===dt?(ot(e,!0),e.strm.avail_out===0?bn:Ai):e.sym_next&&(ot(e,!1),e.strm.avail_out===0)?De:Mi},gi=(e,t)=>{let r,n,i;for(;;){if(e.lookahead<Vt){if(xi(e),e.lookahead<Vt&&t===Vr)return De;if(e.lookahead===0)break}if(r=0,e.lookahead>=V&&(e.ins_h=Ur(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=V-1,r!==0&&e.prev_length<e.max_lazy_match&&e.strstart-r<=e.w_size-Vt&&(e.match_length=UM(e,r),e.match_length<=5&&(e.strategy===iW||e.match_length===V&&e.strstart-e.match_start>4096)&&(e.match_length=V-1)),e.prev_length>=V&&e.match_length<=e.prev_length){i=e.strstart+e.lookahead-V,n=Hr(e,e.strstart-1-e.prev_match,e.prev_length-V),e.lookahead-=e.prev_length-1,e.prev_length-=2;do++e.strstart<=i&&(e.ins_h=Ur(e,e.ins_h,e.window[e.strstart+V-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart);while(--e.prev_length!==0);if(e.match_available=0,e.match_length=V-1,e.strstart++,n&&(ot(e,!1),e.strm.avail_out===0))return De}else if(e.match_available){if(n=Hr(e,0,e.window[e.strstart-1]),n&&ot(e,!1),e.strstart++,e.lookahead--,e.strm.avail_out===0)return De}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Hr(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<V-1?e.strstart:V-1,t===dt?(ot(e,!0),e.strm.avail_out===0?bn:Ai):e.sym_next&&(ot(e,!1),e.strm.avail_out===0)?De:Mi},SW=(e,t)=>{let r,n,i,o,a=e.window;for(;;){if(e.lookahead<=zr){if(xi(e),e.lookahead<=zr&&t===Vr)return 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r=Bo.deflateInit2(this.strm,t.level,t.method,t.windowBits,t.memLevel,t.strategy);if(r!==Uc)throw new Error(_n[r]);if(t.header&&Bo.deflateSetHeader(this.strm,t.header),t.dictionary){let n;if(typeof t.dictionary=="string"?n=Yo.string2buf(t.dictionary):KM.call(t.dictionary)==="[object ArrayBuffer]"?n=new Uint8Array(t.dictionary):n=t.dictionary,r=Bo.deflateSetDictionary(this.strm,n),r!==Uc)throw new Error(_n[r]);this._dict_set=!0}}Jo.prototype.push=function(e,t){let r=this.strm,n=this.options.chunkSize,i,o;if(this.ended)return!1;for(t===~~t?o=t:o=t===!0?KW:YW,typeof e=="string"?r.input=Yo.string2buf(e):KM.call(e)==="[object ArrayBuffer]"?r.input=new Uint8Array(e):r.input=e,r.next_in=0,r.avail_in=r.input.length;;){if(r.avail_out===0&&(r.output=new Uint8Array(n),r.next_out=0,r.avail_out=n),(o===XW||o===ZW)&&r.avail_out<=6){this.onData(r.output.subarray(0,r.next_out)),r.avail_out=0;continue}if(i=Bo.deflate(r,o),i===JW)return r.next_out>0&&this.onData(r.output.subarray(0,r.next_out)),i=Bo.deflateEnd(this.strm),this.onEnd(i),this.ended=!0,i===Uc;if(r.avail_out===0){this.onData(r.output);continue}if(o>0&&r.next_out>0){this.onData(r.output.subarray(0,r.next_out)),r.avail_out=0;continue}if(r.avail_in===0)break}return!0};Jo.prototype.onData=function(e){this.chunks.push(e)};Jo.prototype.onEnd=function(e){e===Uc&&(this.result=$c.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};function Yh(e,t){let r=new Jo(t);if(r.push(e,!0),r.err)throw r.msg||_n[r.err];return r.result}function rG(e,t){return t=t||{},t.raw=!0,Yh(e,t)}function nG(e,t){return t=t||{},t.gzip=!0,Yh(e,t)}var iG=Jo,oG=Yh,aG=rG,uG=nG,sG=Oi,lG={Deflate:iG,deflate:oG,deflateRaw:aG,gzip:uG,constants:sG},Dc=16209,cG=16191,fG=function(t,r){let n,i,o,a,u,f,l,d,s,c,p,m,v,h,_,y,w,S,E,O,A,q,M,P,k=t.state;n=t.next_in,M=t.input,i=n+(t.avail_in-5),o=t.next_out,P=t.output,a=o-(r-t.avail_out),u=o+(t.avail_out-257),f=k.dmax,l=k.wsize,d=k.whave,s=k.wnext,c=k.window,p=k.hold,m=k.bits,v=k.lencode,h=k.distcode,_=(1<<k.lenbits)-1,y=(1<<k.distbits)-1;e:do{m<15&&(p+=M[n++]<<m,m+=8,p+=M[n++]<<m,m+=8),w=v[p&_];t:for(;;){if(S=w>>>24,p>>>=S,m-=S,S=w>>>16&255,S===0)P[o++]=w&65535;else if(S&16){E=w&65535,S&=15,S&&(m<S&&(p+=M[n++]<<m,m+=8),E+=p&(1<<S)-1,p>>>=S,m-=S),m<15&&(p+=M[n++]<<m,m+=8,p+=M[n++]<<m,m+=8),w=h[p&y];r:for(;;){if(S=w>>>24,p>>>=S,m-=S,S=w>>>16&255,S&16){if(O=w&65535,S&=15,m<S&&(p+=M[n++]<<m,m+=8,m<S&&(p+=M[n++]<<m,m+=8)),O+=p&(1<<S)-1,O>f){t.msg="invalid distance too far back",k.mode=Dc;break e}if(p>>>=S,m-=S,S=o-a,O>S){if(S=O-S,S>d&&k.sane){t.msg="invalid distance too far back",k.mode=Dc;break e}if(A=0,q=c,s===0){if(A+=l-S,S<E){E-=S;do P[o++]=c[A++];while(--S);A=o-O,q=P}}else if(s<S){if(A+=l+s-S,S-=s,S<E){E-=S;do P[o++]=c[A++];while(--S);if(A=0,s<E){S=s,E-=S;do P[o++]=c[A++];while(--S);A=o-O,q=P}}}else if(A+=s-S,S<E){E-=S;do P[o++]=c[A++];while(--S);A=o-O,q=P}for(;E>2;)P[o++]=q[A++],P[o++]=q[A++],P[o++]=q[A++],E-=3;E&&(P[o++]=q[A++],E>1&&(P[o++]=q[A++]))}else{A=o-O;do P[o++]=P[A++],P[o++]=P[A++],P[o++]=P[A++],E-=3;while(E>2);E&&(P[o++]=P[A++],E>1&&(P[o++]=P[A++]))}}else if(S&64){t.msg="invalid distance code",k.mode=Dc;break e}else{w=h[(w&65535)+(p&(1<<S)-1)];continue r}break}}else if(S&64)if(S&32){k.mode=cG;break e}else{t.msg="invalid literal/length code",k.mode=Dc;break e}else{w=v[(w&65535)+(p&(1<<S)-1)];continue t}break}}while(n<i&&o<u);E=m>>3,n-=E,m-=E<<3,p&=(1<<m)-1,t.next_in=n,t.next_out=o,t.avail_in=n<i?5+(i-n):5-(n-i),t.avail_out=o<u?257+(u-o):257-(o-u),k.hold=p,k.bits=m},yi=15,QO=852,eM=592,tM=0,Mh=1,rM=2,dG=new Uint16Array([3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),pG=new Uint8Array([16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78]),hG=new Uint16Array([1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0]),mG=new Uint8Array([16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64]),vG=(e,t,r,n,i,o,a,u)=>{let f=u.bits,l=0,d=0,s=0,c=0,p=0,m=0,v=0,h=0,_=0,y=0,w,S,E,O,A,q=null,M,P=new Uint16Array(yi+1),k=new Uint16Array(yi+1),R=null,$,B,ie;for(l=0;l<=yi;l++)P[l]=0;for(d=0;d<n;d++)P[t[r+d]]++;for(p=f,c=yi;c>=1&&P[c]===0;c--);if(p>c&&(p=c),c===0)return i[o++]=1<<24|64<<16|0,i[o++]=1<<24|64<<16|0,u.bits=1,0;for(s=1;s<c&&P[s]===0;s++);for(p<s&&(p=s),h=1,l=1;l<=yi;l++)if(h<<=1,h-=P[l],h<0)return-1;if(h>0&&(e===tM||c!==1))return-1;for(k[1]=0,l=1;l<yi;l++)k[l+1]=k[l]+P[l];for(d=0;d<n;d++)t[r+d]!==0&&(a[k[t[r+d]]++]=d);if(e===tM?(q=R=a,M=20):e===Mh?(q=dG,R=pG,M=257):(q=hG,R=mG,M=0),y=0,d=0,l=s,A=o,m=p,v=0,E=-1,_=1<<p,O=_-1,e===Mh&&_>QO||e===rM&&_>eM)return 1;for(;;){$=l-v,a[d]+1<M?(B=0,ie=a[d]):a[d]>=M?(B=R[a[d]-M],ie=q[a[d]-M]):(B=96,ie=0),w=1<<l-v,S=1<<m,s=S;do S-=w,i[A+(y>>v)+S]=$<<24|B<<16|ie|0;while(S!==0);for(w=1<<l-1;y&w;)w>>=1;if(w!==0?(y&=w-1,y+=w):y=0,d++,--P[l]===0){if(l===c)break;l=t[r+a[d]]}if(l>p&&(y&O)!==E){for(v===0&&(v=p),A+=s,m=l-v,h=1<<m;m+v<c&&(h-=P[m+v],!(h<=0));)m++,h<<=1;if(_+=1<<m,e===Mh&&_>QO||e===rM&&_>eM)return 1;E=y&O,i[E]=p<<24|m<<16|A-o|0}}return y!==0&&(i[A+y]=l-v<<24|64<<16|0),u.bits=p,0},zo=vG,_G=0,JM=1,QM=2,{Z_FINISH:nM,Z_BLOCK:bG,Z_TREES:Nc,Z_OK:gn,Z_STREAM_END:gG,Z_NEED_DICT:yG,Z_STREAM_ERROR:pt,Z_DATA_ERROR:e2,Z_MEM_ERROR:t2,Z_BUF_ERROR:wG,Z_DEFLATED:iM}=Oi,Yc=16180,oM=16181,aM=16182,uM=16183,sM=16184,lM=16185,cM=16186,fM=16187,dM=16188,pM=16189,Wc=16190,sr=16191,Ah=16192,hM=16193,Ph=16194,mM=16195,vM=16196,_M=16197,bM=16198,Bc=16199,zc=16200,gM=16201,yM=16202,wM=16203,SM=16204,xM=16205,qh=16206,EM=16207,OM=16208,ne=16209,r2=16210,n2=16211,SG=852,xG=592,EG=15,OG=EG,MM=e=>(e>>>24&255)+(e>>>8&65280)+((e&65280)<<8)+((e&255)<<24);function MG(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}var yn=e=>{if(!e)return 1;let t=e.state;return!t||t.strm!==e||t.mode<Yc||t.mode>n2?1:0},i2=e=>{if(yn(e))return pt;let t=e.state;return e.total_in=e.total_out=t.total=0,e.msg="",t.wrap&&(e.adler=t.wrap&1),t.mode=Yc,t.last=0,t.havedict=0,t.flags=-1,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(SG),t.distcode=t.distdyn=new Int32Array(xG),t.sane=1,t.back=-1,gn},o2=e=>{if(yn(e))return pt;let t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,i2(e)},a2=(e,t)=>{let r;if(yn(e))return pt;let n=e.state;return t<0?(r=0,t=-t):(r=(t>>4)+5,t<48&&(t&=15)),t&&(t<8||t>15)?pt:(n.window!==null&&n.wbits!==t&&(n.window=null),n.wrap=r,n.wbits=t,o2(e))},u2=(e,t)=>{if(!e)return pt;let r=new MG;e.state=r,r.strm=e,r.window=null,r.mode=Yc;let n=a2(e,t);return n!==gn&&(e.state=null),n},AG=e=>u2(e,OG),AM=!0,kh,Th,PG=e=>{if(AM){kh=new Int32Array(512),Th=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(zo(JM,e.lens,0,288,kh,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;zo(QM,e.lens,0,32,Th,0,e.work,{bits:5}),AM=!1}e.lencode=kh,e.lenbits=9,e.distcode=Th,e.distbits=5},s2=(e,t,r,n)=>{let i,o=e.state;return o.window===null&&(o.wsize=1<<o.wbits,o.wnext=0,o.whave=0,o.window=new Uint8Array(o.wsize)),n>=o.wsize?(o.window.set(t.subarray(r-o.wsize,r),0),o.wnext=0,o.whave=o.wsize):(i=o.wsize-o.wnext,i>n&&(i=n),o.window.set(t.subarray(r-n,r-n+i),o.wnext),n-=i,n?(o.window.set(t.subarray(r-n,r),0),o.wnext=n,o.whave=o.wsize):(o.wnext+=i,o.wnext===o.wsize&&(o.wnext=0),o.whave<o.wsize&&(o.whave+=i))),0},qG=(e,t)=>{let r,n,i,o,a,u,f,l,d,s,c,p,m,v,h=0,_,y,w,S,E,O,A,q,M=new Uint8Array(4),P,k,R=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(yn(e)||!e.output||!e.input&&e.avail_in!==0)return pt;r=e.state,r.mode===sr&&(r.mode=Ah),a=e.next_out,i=e.output,f=e.avail_out,o=e.next_in,n=e.input,u=e.avail_in,l=r.hold,d=r.bits,s=u,c=f,q=gn;e:for(;;)switch(r.mode){case Yc:if(r.wrap===0){r.mode=Ah;break}for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.wrap&2&&l===35615){r.wbits===0&&(r.wbits=15),r.check=0,M[0]=l&255,M[1]=l>>>8&255,r.check=we(r.check,M,2,0),l=0,d=0,r.mode=oM;break}if(r.head&&(r.head.done=!1),!(r.wrap&1)||(((l&255)<<8)+(l>>8))%31){e.msg="incorrect header check",r.mode=ne;break}if((l&15)!==iM){e.msg="unknown compression method",r.mode=ne;break}if(l>>>=4,d-=4,A=(l&15)+8,r.wbits===0&&(r.wbits=A),A>15||A>r.wbits){e.msg="invalid window size",r.mode=ne;break}r.dmax=1<<r.wbits,r.flags=0,e.adler=r.check=1,r.mode=l&512?pM:sr,l=0,d=0;break;case oM:for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.flags=l,(r.flags&255)!==iM){e.msg="unknown compression method",r.mode=ne;break}if(r.flags&57344){e.msg="unknown header flags set",r.mode=ne;break}r.head&&(r.head.text=l>>8&1),r.flags&512&&r.wrap&4&&(M[0]=l&255,M[1]=l>>>8&255,r.check=we(r.check,M,2,0)),l=0,d=0,r.mode=aM;case aM:for(;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.time=l),r.flags&512&&r.wrap&4&&(M[0]=l&255,M[1]=l>>>8&255,M[2]=l>>>16&255,M[3]=l>>>24&255,r.check=we(r.check,M,4,0)),l=0,d=0,r.mode=uM;case uM:for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.xflags=l&255,r.head.os=l>>8),r.flags&512&&r.wrap&4&&(M[0]=l&255,M[1]=l>>>8&255,r.check=we(r.check,M,2,0)),l=0,d=0,r.mode=sM;case sM:if(r.flags&1024){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.length=l,r.head&&(r.head.extra_len=l),r.flags&512&&r.wrap&4&&(M[0]=l&255,M[1]=l>>>8&255,r.check=we(r.check,M,2,0)),l=0,d=0}else r.head&&(r.head.extra=null);r.mode=lM;case lM:if(r.flags&1024&&(p=r.length,p>u&&(p=u),p&&(r.head&&(A=r.head.extra_len-r.length,r.head.extra||(r.head.extra=new Uint8Array(r.head.extra_len)),r.head.extra.set(n.subarray(o,o+p),A)),r.flags&512&&r.wrap&4&&(r.check=we(r.check,n,p,o)),u-=p,o+=p,r.length-=p),r.length))break e;r.length=0,r.mode=cM;case cM:if(r.flags&2048){if(u===0)break e;p=0;do A=n[o+p++],r.head&&A&&r.length<65536&&(r.head.name+=String.fromCharCode(A));while(A&&p<u);if(r.flags&512&&r.wrap&4&&(r.check=we(r.check,n,p,o)),u-=p,o+=p,A)break e}else r.head&&(r.head.name=null);r.length=0,r.mode=fM;case fM:if(r.flags&4096){if(u===0)break e;p=0;do A=n[o+p++],r.head&&A&&r.length<65536&&(r.head.comment+=String.fromCharCode(A));while(A&&p<u);if(r.flags&512&&r.wrap&4&&(r.check=we(r.check,n,p,o)),u-=p,o+=p,A)break e}else r.head&&(r.head.comment=null);r.mode=dM;case dM:if(r.flags&512){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.wrap&4&&l!==(r.check&65535)){e.msg="header crc mismatch",r.mode=ne;break}l=0,d=0}r.head&&(r.head.hcrc=r.flags>>9&1,r.head.done=!0),e.adler=r.check=0,r.mode=sr;break;case pM:for(;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}e.adler=r.check=MM(l),l=0,d=0,r.mode=Wc;case Wc:if(r.havedict===0)return e.next_out=a,e.avail_out=f,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,yG;e.adler=r.check=1,r.mode=sr;case sr:if(t===bG||t===Nc)break e;case Ah:if(r.last){l>>>=d&7,d-=d&7,r.mode=qh;break}for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}switch(r.last=l&1,l>>>=1,d-=1,l&3){case 0:r.mode=hM;break;case 1:if(PG(r),r.mode=Bc,t===Nc){l>>>=2,d-=2;break e}break;case 2:r.mode=vM;break;case 3:e.msg="invalid block type",r.mode=ne}l>>>=2,d-=2;break;case hM:for(l>>>=d&7,d-=d&7;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if((l&65535)!==(l>>>16^65535)){e.msg="invalid stored block lengths",r.mode=ne;break}if(r.length=l&65535,l=0,d=0,r.mode=Ph,t===Nc)break e;case Ph:r.mode=mM;case mM:if(p=r.length,p){if(p>u&&(p=u),p>f&&(p=f),p===0)break e;i.set(n.subarray(o,o+p),a),u-=p,o+=p,f-=p,a+=p,r.length-=p;break}r.mode=sr;break;case vM:for(;d<14;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.nlen=(l&31)+257,l>>>=5,d-=5,r.ndist=(l&31)+1,l>>>=5,d-=5,r.ncode=(l&15)+4,l>>>=4,d-=4,r.nlen>286||r.ndist>30){e.msg="too many length or distance symbols",r.mode=ne;break}r.have=0,r.mode=_M;case _M:for(;r.have<r.ncode;){for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.lens[R[r.have++]]=l&7,l>>>=3,d-=3}for(;r.have<19;)r.lens[R[r.have++]]=0;if(r.lencode=r.lendyn,r.lenbits=7,P={bits:r.lenbits},q=zo(_G,r.lens,0,19,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid code lengths set",r.mode=ne;break}r.have=0,r.mode=bM;case bM:for(;r.have<r.nlen+r.ndist;){for(;h=r.lencode[l&(1<<r.lenbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(w<16)l>>>=_,d-=_,r.lens[r.have++]=w;else{if(w===16){for(k=_+2;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(l>>>=_,d-=_,r.have===0){e.msg="invalid bit length repeat",r.mode=ne;break}A=r.lens[r.have-1],p=3+(l&3),l>>>=2,d-=2}else if(w===17){for(k=_+3;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,p=3+(l&7),l>>>=3,d-=3}else{for(k=_+7;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,p=11+(l&127),l>>>=7,d-=7}if(r.have+p>r.nlen+r.ndist){e.msg="invalid bit length 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  /*! Bundled license information:
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  canvas2svg/canvas2svg.js: