jbrowse-plugin-msaview 2.0.2 → 2.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/MsaViewPanel/model.d.ts +62 -19
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +22 -22
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/ncbiBlast.js +2 -2
- package/dist/utils/ncbiBlast.js.map +1 -1
- package/package.json +4 -4
- package/src/utils/ncbiBlast.ts +2 -2
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"use strict";var JBrowsePluginMsaView=(()=>{var
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"use strict";var JBrowsePluginMsaView=(()=>{var I2=Object.create;var na=Object.defineProperty;var L2=Object.getOwnPropertyDescriptor;var R2=Object.getOwnPropertyNames;var F2=Object.getPrototypeOf,D2=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),at=(e,t)=>{for(var r in t)na(e,r,{get:t[r],enumerable:!0})},um=(e,t,r,n)=>{if(t&&typeof t=="object"||typeof t=="function")for(let i of R2(t))!D2.call(e,i)&&i!==r&&na(e,i,{get:()=>t[i],enumerable:!(n=L2(t,i))||n.enumerable});return e};var S=(e,t,r)=>(r=e!=null?I2(F2(e)):{},um(t||!e||!e.__esModule?na(r,"default",{value:e,enumerable:!0}):r,e)),N2=e=>um(na({},"__esModule",{value:!0}),e);var lm=g((P$,sm)=>{sm.exports=JBrowseExports["@jbrowse/core/Plugin"]});var we=g((q$,cm)=>{cm.exports=JBrowseExports["@jbrowse/core/util"]});var J=g((k$,Ci)=>{function B2(e){return e&&e.__esModule?e:{default:e}}Ci.exports=B2,Ci.exports.__esModule=!0,Ci.exports.default=Ci.exports});var dm=g((T$,fm)=>{fm.exports=JBrowseExports["@mui/material/utils"]});var re=g(rf=>{"use strict";"use client";Object.defineProperty(rf,"__esModule",{value:!0});Object.defineProperty(rf,"default",{enumerable:!0,get:function(){return z2.createSvgIcon}});var z2=dm()});var ne=g((j$,hm)=>{hm.exports=JBrowseExports["react/jsx-runtime"]});var pm=g(ia=>{"use strict";"use client";var H2=J();Object.defineProperty(ia,"__esModule",{value:!0});ia.default=void 0;var V2=H2(re()),U2=ne(),I$=ia.default=(0,V2.default)((0,U2.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((F$,vm)=>{vm.exports=JBrowseExports.react});var bm=g((D$,_m)=>{_m.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes/ViewType"]});var Gt=g((N$,gm)=>{gm.exports=JBrowseExports["mobx-state-tree"]});var $t=g((B$,ym)=>{ym.exports=JBrowseExports.mobx});var N=g((z$,wm)=>{wm.exports=JBrowseExports["mobx-react"]});var z=g((H$,Sm)=>{Sm.exports=JBrowseExports["@mui/material"]});function $2(){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 Ze,G2,nf,oa,xm=C(()=>{"use client";Ze=S(I()),G2=(0,Ze.createContext)(null),nf={didCatch:!1,error:null},oa=class extends Ze.Component{constructor(t){super(t),this.resetErrorBoundary=this.resetErrorBoundary.bind(this),this.state=nf}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(nf)}}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&&$2(t.resetKeys,i)){var o,a;(o=(a=this.props).onReset)===null||o===void 0||o.call(a,{next:i,prev:t.resetKeys,reason:"keys"}),this.setState(nf)}}render(){let{children:t,fallbackRender:r,FallbackComponent:n,fallback:i}=this.props,{didCatch:o,error:a}=this.state,u=t;if(o){let f={error:a,resetErrorBoundary:this.resetErrorBoundary};if(typeof r=="function")u=r(f);else if(n)u=(0,Ze.createElement)(n,f);else if(i===null||(0,Ze.isValidElement)(i))u=i;else throw a}return(0,Ze.createElement)(G2.Provider,{value:{didCatch:o,error:a,resetErrorBoundary:this.resetErrorBoundary}},u)}}});var Se=g((U$,Em)=>{Em.exports=JBrowseExports["@jbrowse/core/ui"]});async function Mt(e,t,r){e.setError(void 0),t&&e.setMSAFilehandle(t),r&&e.setTreeFilehandle(r)}var of=C(()=>{});var Mm,Om,Am,Pm=C(()=>{Mm=`CLUSTAL O(1.2.3) multiple sequence alignment
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UniProt/Swiss-Prot|P26898|IL2RA_SHEEP MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
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UniProt/Swiss-Prot|P01590|IL2RA_MOUSE MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
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UniProt/Swiss-Prot|P41690|IL2RA_FELCA MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
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@@ -11,7 +11,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE PLPLRSLLFLQLPLLGVGLNP----------------
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UniProt/Swiss-Prot|P36835|IL2_CAPHI -----------LLGVGLNPKFLTP------------------------------------
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UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
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UniProt/Swiss-Prot|Q29416|IL2_CANFA --------------LFLQLSLLG-------------------------------------
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`,
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`,Om=`CLUSTAL O(1.2.4) multiple sequence alignment
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sp|P69905|HBA_HUMAN MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG 60
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@@ -27,35 +27,35 @@ sp|P13786|HBAZ_CAPHI SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
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sp|P69905|HBA_HUMAN AVHASLDKFLASVSTVLTSKYR 142
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sp|P01942|HBA_MOUSE AVHASLDKFLASVSTVLTSKYR 142
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sp|P13786|HBAZ_CAPHI DAHAAWDKFLSIVSGVLTEKYR 142
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.**: ****: ** ***.***`,Sm="(((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 Be,oa,Em,Gt,V2,Om,Mm=C(()=>{Be=x(I()),oa=x(N()),Em=x(D());xm();rf();Gt=({onClick:e,model:t,children:r})=>Be.default.createElement("li",null,Be.default.createElement(oa.Link,{onClick:n=>{t.setError(void 0),n.preventDefault(),e()},href:"#"},Be.default.createElement(oa.Typography,{display:"inline"},r))),V2=(0,Em.observer)(function({model:e}){return Be.default.createElement("ul",null,Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,void 0,{uri:"https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh",locationType:"UriLocation"})},"230k COVID-19 samples (tree only)"),Be.default.createElement(Gt,{model:e,onClick:()=>{e.setData({msa:ym,tree:Sm})}},"Small protein MSA+tree"),Be.default.createElement(Gt,{model:e,onClick:()=>{e.setData({msa:wm})}},"Small MSA only"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock",locationType:"UriLocation"})},"PFAM SARS-CoV2 multi-stockholm"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock",locationType:"UriLocation"})},"Lysine stockholm file"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt",locationType:"UriLocation"})},"PF01601 stockholm file (SARS-CoV2 spike protein)"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa",locationType:"UriLocation"})},"Europe COVID full genomes (LR883044.1 and 199 other sequences)"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(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)"),Be.default.createElement(Gt,{model:e,onClick:()=>Ot(e,{uri:"https://jbrowse.org/demos/ttc39a.mfa",locationType:"UriLocation"})},"Human BLAST results mfa"))}),Om=V2});var ce,Am,ke,nf,Pm,qm=C(()=>{ce=x(I()),Am=x(D()),ke=x(N()),nf=x(qe());rf();Mm();Pm=(0,Am.observer)(({model:e})=>{let[t,r]=(0,ce.useState)(),[n,i]=(0,ce.useState)(),{error:o}=e;return ce.default.createElement(ke.Container,null,ce.default.createElement("div",{style:{width:"50%"}},o?ce.default.createElement("div",{style:{padding:20}},ce.default.createElement(ke.Typography,{color:"error"},"Error: ",`${o}`)):null,ce.default.createElement(ke.Typography,null,"Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),ce.default.createElement(ke.Typography,{color:"error"},"Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),ce.default.createElement(ke.Grid,{container:!0,spacing:10,justifyContent:"center",alignItems:"center"},ce.default.createElement(ke.Grid,{item:!0},ce.default.createElement(ke.Typography,null,"MSA file or URL"),ce.default.createElement(nf.FileSelector,{location:t,setLocation:r}),ce.default.createElement(ke.Typography,null,"Tree file or URL"),ce.default.createElement(nf.FileSelector,{location:n,setLocation:i})),ce.default.createElement(ke.Grid,{item:!0},ce.default.createElement(ke.Button,{onClick:()=>Ot(e,t,n),variant:"contained",color:"primary",disabled:!t&&!n},"Open")),ce.default.createElement(ke.Grid,{item:!0},ce.default.createElement(ke.Typography,null,"Examples"),ce.default.createElement(Om,{model:e}))))})});var 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qH({seq:e,onProgress:t,onJobId:r,programs:n,model:i}){let o=await kh(`${Ih}/iprscan5/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",sequence:`${e}`,programs:n.join(",")})});return r?.(o),await TH({jobId:o,onProgress:t}),CH({jobId:o,model:i})}function kH(e){return fc(`${Ih}/iprscan5/result/${e}/json`)}async function TH({onProgress:e,jobId:t}){let r=`${Ih}/iprscan5/status/${t}`;try{for(;;){for(let i=0;i<10;i++)await Hw(1e3),e({msg:`Checking status ${10-i}`,url:r});let n=await kh(r);if(n.includes("FINISHED"))break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}finally{e()}}async function $w({algorithm:e,seq:t,programs:r,onJobId:n,onProgress:i,model:o}){try{if(i({msg:`Launching ${e} MSA`}),e==="interproscan")return await qH({seq:t,onJobId:n,onProgress:i,programs:r,model:o});throw new Error("unknown algorithm")}finally{i()}}async function CH({jobId:e,model:t}){try{t.setStatus({msg:`Downloading results of ${e} (for larger sequences this 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-
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|
|
38
|
+
`).forEach((u,f)=>{let l=()=>{o||(n(wc(f)+Qx),o=new ce)},d;tE.test(u)?(o&&n(wc(f)+DV),o=new ce):TV.test(u)?(o?i.push(o):n(wc(f)+Qx),o=null):(d=CV.exec(u))?(l(),o.gf[d[1]]=o.gf[d[1]]||[],o.gf[d[1]].push(d[2])):(d=jV.exec(u))?(l(),o.gc[d[1]]=o.gc[d[1]]||"",o.gc[d[1]]+=d[2]):(d=IV.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=LV.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=RV.exec(u))?(l(),o.seqdata[d[1]]||(o.seqdata[d[1]]="",o.seqname.push(d[1])),o.seqdata[d[1]]+=d[2]):FV.test(u)&&lr(wc(f)+NV)}),o&&(n("Warning: no end line //"),i.push(o)),i},VV=(e,t)=>{let r=Zh(e,t);return r.length===0&&lr("No alignments found"),r.length>1&&lr("More than one alignment found"),r[0]},UV=(e,t)=>{let r=new ce;return t=t||Object.keys(e),t.forEach(n=>r.addRow(n,e[n])),r},WV=e=>{let t=new ce;return e.forEach(r=>t.addRow(r[0],r[1])),t};ce.prototype.rows=function(){return this.seqname.length};ce.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};ce.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};ce.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()};ce.prototype.addRow=function(e,t){return this.seqdata[e]&&lr("Duplicate row name"),this.seqname.push(e),this.seqdata[e]=t||"",this};ce.prototype.deleteRow=function(e){return this.seqdata[e]||lr("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 xc=(e,t)=>{let r={};return Object.keys(e).forEach(n=>r[n]=t(e[n])),r},Po=e=>xc(e,t=>t.slice(0)),$h=e=>xc(e,t=>Po(t));ce.prototype.copy=function(){let e=new ce;return e.seqname=this.seqname.slice(0),e.seqdata=Po(this.seqdata),e.gf=Po(this.gf),e.gc=Po(this.gc),e.gs=$h(this.gs),e.gr=$h(this.gr),e};var GV=(e,t)=>t.map(r=>e[r]).join(""),Yh=(e,t)=>xc(e,r=>GV(r,t)),$V=(e,t)=>xc(e,r=>Yh(r,t));ce.prototype.extractColumns=function(e){let t=this.columns(),r=e.filter(i=>i<0||i>=t);r.length&&lr("Bad column indices: "+r.join(","));let n=new ce;return n.seqname=this.seqname.slice(0),n.seqdata=Yh(this.seqdata,e),n.gf=Po(this.gf),n.gc=Yh(this.gc,e),n.gs=$h(this.gs),n.gr=$V(this.gr,e),n};ce.prototype.extractColumnRange=function(e,t){return this.extractColumns(new Array(t+1-e).fill(0).map((r,n)=>e+n))};ce.prototype.defaultGapChars=".-";ce.prototype.seqpos2col=function(e,t){t=t||this.defaultGapChars,this.seqdata[e]||lr("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)};ce.prototype.col2seqpos=function(e,t){t=t||this.defaultGapChars,this.seqdata[e]||lr("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 Sc(e,t){for(;e.length<t;)e=" "+e;return e}function eE(e,t){for(;e.length<t;)e=e+" ";return e}function YV(e){return Sc("",e)}ce.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?Sc:eE,f=e.indentNames?(d,s)=>Sc(d,i)+" "+Sc(s,n):(d,s)=>eE(d+" "+s,i+n+1),l=[0];for(let d=a;d<r;d+=a)l.push(d);return`# STOCKHOLM 1.0
|
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39
39
|
`+Object.keys(this.gf).sort().map(d=>this.gf[d].map(s=>"#=GF "+u(d,i)+" "+s+`
|
|
40
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+`
|
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41
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-
`).join("")).join("")).join("")+l.map(d=>Object.keys(this.gc).sort().map(s=>"#=GC "+u(s,i)+
|
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41
|
+
`).join("")).join("")).join("")+l.map(d=>Object.keys(this.gc).sort().map(s=>"#=GC "+u(s,i)+YV(n+2)+this.gc[s].substr(d,a)+`
|
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42
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)+`
|
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43
43
|
`).join("")+(this.seqdata[s]?u(s,n+o)+" "+this.seqdata[s].substr(d,a)+`
|
|
44
44
|
`:"")).join("")).join(`
|
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45
45
|
`)+`//
|
|
46
|
-
`};
|
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46
|
+
`};ce.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+`
|
|
47
47
|
`+n.map(o=>this.seqdata[i].substr(o,r)+`
|
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48
|
-
`).join(""):"").join("")};le.prototype.toRowList=function(e){return this.allNames().filter(t=>this.seqdata[t]).map(t=>[t,this.seqdata[t]])};typeof Wp<"u"&&(Wp.exports={sniff:PV,validate:qV,parse:TV,parseAll:Gp,fromSeqIndex:CV,fromRowList:jV,Stockholm:le})});var $p=g((Dte,Kx)=>{Kx.exports=Zx()});var Jx=g((Yp,Xp)=>{(function(e,t){typeof define=="function"&&define.amd?define([],t):typeof Yp<"u"?t():(t(),e.FileSaver={})})(Yp,function(){"use strict";function e(u,f){return typeof f>"u"?f={autoBom:!1}:typeof f!="object"&&(console.warn("Deprecated: Expected third argument to be a object"),f={autoBom:!f}),f.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,f,l){var d=new XMLHttpRequest;d.open("GET",u),d.responseType="blob",d.onload=function(){a(d.response,f,l)},d.onerror=function(){console.error("could not download file")},d.send()}function r(u){var f=new 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q=E*u+r-r%u;_.fillStyle=A||"white",_.fillRect(q,0,u,l),l>=10&&u>=l/2&&(_.fillStyle=h[O.toUpperCase()]||"black",_.fillText(O,q+u/2,l/2+1))}}},[f,o,n,u,l,r,h,p,d,c]),Dt.default.createElement("canvas",{ref:v,height:l*d,width:n*d,style:{position:"absolute",left:i+r,width:n,height:l}})}),DV=(0,Jp.observer)(function({track:e,model:t}){let{blocksX:r,msaAreaWidth:n,rowHeight:i}=t;return Dt.default.createElement("div",{style:{position:"relative",height:i,width:n,overflow:"hidden"}},r.map(o=>Dt.default.createElement(FV,{key:o,track:e,model:t,offsetX:o})))}),cE=DV});var eh=g(Ge=>{"use strict";Object.defineProperty(Ge,"__esModule",{value:!0});Ge.parseBlocks=Ge.parseBlock=Ge.getSeqBounds=Ge.getFirstNonEmptyLine=Ge.parseHeader=Ge.parseVersion=void 0;function dE(e){let t=e.match(/\(?(\d+(\.\d+)+)\)?/);return t&&t.length>1?t[1]:""}Ge.parseVersion=dE;function NV(e){let t=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];t.some(n=>e.startsWith(n))||console.warn(`${e} is not a known CLUSTAL header: 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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. Con ${o.length} seq ${i[0].seq.length}`);return{consensus:o,alns:i,header:r}}Nt.parseClustalIter=_E;function bE(e){let t=(0,VV.parsePairwiseBlocks)(e.split(`
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49
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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}}
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50
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-
`)[Symbol.iterator]();return
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+
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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]),qc=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]),eU=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),YE=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),tU=512,fr=new Array((Lo+2)*2);Ei(fr);Co=new Array(wi*2);Ei(Co);Ro=new Array(tU);Ei(Ro);Fo=new Array(JV-KV+1);Ei(Fo);Op=new Array(xp);Ei(Op);kc=new Array(wi);Ei(kc);JE=e=>e<256?Ro[e]:Ro[256+(e>>>7)],Do=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},Ge=(e,t,r)=>{e.bi_valid>ep-r?(e.bi_buf|=t<<e.bi_valid&65535,Do(e,e.bi_buf),e.bi_buf=t>>ep-e.bi_valid,e.bi_valid+=r-ep):(e.bi_buf|=t<<e.bi_valid&65535,e.bi_valid+=r)},zt=(e,t,r)=>{Ge(e,r[t*2],r[t*2+1])},QE=(e,t)=>{let r=0;do r|=e&1,e>>>=1,r<<=1;while(--t>0);return r>>>1},rU=e=>{e.bi_valid===16?(Do(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)},nU=(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,h,m,v=0;for(c=0;c<=vn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<UE;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]++,h=0,d>=u&&(h=a[d-u]),m=r[d*2],e.opt_len+=m*(c+h),o&&(e.static_len+=m*(i[d*2+1]+h)));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--)}},eM=(e,t,r)=>{let n=new Array(vn+1),i=0,o,a;for(o=1;o<=vn;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]=QE(n[u]++,u))}},iU=()=>{let e,t,r,n,i,o=new Array(vn+1);for(r=0,n=0;n<xp-1;n++)for(Op[n]=r,e=0;e<1<<pp[n];e++)Fo[r++]=n;for(Fo[r-1]=n,i=0,n=0;n<16;n++)for(kc[n]=i,e=0;e<1<<qc[n];e++)Ro[i++]=n;for(i>>=7;n<wi;n++)for(kc[n]=i<<7,e=0;e<1<<qc[n]-7;e++)Ro[256+i++]=n;for(t=0;t<=vn;t++)o[t]=0;for(e=0;e<=143;)fr[e*2+1]=8,e++,o[8]++;for(;e<=255;)fr[e*2+1]=9,e++,o[9]++;for(;e<=279;)fr[e*2+1]=7,e++,o[7]++;for(;e<=287;)fr[e*2+1]=8,e++,o[8]++;for(eM(fr,Lo+1,o),e=0;e<wi;e++)Co[e*2+1]=5,Co[e*2]=QE(e,5);XE=new tp(fr,pp,Vo+1,Lo,vn),ZE=new tp(Co,qc,0,wi,vn),KE=new tp(new Array(0),eU,0,Ep,QV)},tM=e=>{let t;for(t=0;t<Lo;t++)e.dyn_ltree[t*2]=0;for(t=0;t<wi;t++)e.dyn_dtree[t*2]=0;for(t=0;t<Ep;t++)e.bl_tree[t*2]=0;e.dyn_ltree[Mp*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},rM=e=>{e.bi_valid>8?Do(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},oE=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},np=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&oE(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!oE(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},aE=(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=Fo[i],zt(e,a+Vo+1,t),u=pp[a],u!==0&&(i-=Op[a],Ge(e,i,u)),n--,a=JE(n),zt(e,a,r),u=qc[a],u!==0&&(n-=kc[a],Ge(e,n,u)));while(o<e.sym_next);zt(e,Mp,t)},mp=(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=UE,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--)np(e,r,a);l=o;do a=e.heap[1],e.heap[1]=e.heap[e.heap_len--],np(e,r,1),u=e.heap[1],e.heap[--e.heap_max]=a,e.heap[--e.heap_max]=u,r[l*2]=r[a*2]+r[u*2],e.depth[l]=(e.depth[a]>=e.depth[u]?e.depth[a]:e.depth[u])+1,r[a*2+1]=r[u*2+1]=l,e.heap[1]=l++,np(e,r,1);while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],nU(e,t),eM(r,f,e.bl_count)},uE=(e,t,r)=>{let n,i=-1,o,a=t[0*2+1],u=0,f=7,l=4;for(a===0&&(f=138,l=3),t[(r+1)*2+1]=65535,n=0;n<=r;n++)o=a,a=t[(n+1)*2+1],!(++u<f&&o===a)&&(u<l?e.bl_tree[o*2]+=u:o!==0?(o!==i&&e.bl_tree[o*2]++,e.bl_tree[WE*2]++):u<=10?e.bl_tree[GE*2]++:e.bl_tree[$E*2]++,u=0,i=o,a===0?(f=138,l=3):o===a?(f=6,l=3):(f=7,l=4))},sE=(e,t,r)=>{let n,i=-1,o,a=t[0*2+1],u=0,f=7,l=4;for(a===0&&(f=138,l=3),n=0;n<=r;n++)if(o=a,a=t[(n+1)*2+1],!(++u<f&&o===a)){if(u<l)do zt(e,o,e.bl_tree);while(--u!==0);else o!==0?(o!==i&&(zt(e,o,e.bl_tree),u--),zt(e,WE,e.bl_tree),Ge(e,u-3,2)):u<=10?(zt(e,GE,e.bl_tree),Ge(e,u-3,3)):(zt(e,$E,e.bl_tree),Ge(e,u-11,7));u=0,i=o,a===0?(f=138,l=3):o===a?(f=6,l=3):(f=7,l=4)}},oU=e=>{let t;for(uE(e,e.dyn_ltree,e.l_desc.max_code),uE(e,e.dyn_dtree,e.d_desc.max_code),mp(e,e.bl_desc),t=Ep-1;t>=3&&e.bl_tree[YE[t]*2+1]===0;t--);return e.opt_len+=3*(t+1)+5+5+4,t},aU=(e,t,r,n)=>{let i;for(Ge(e,t-257,5),Ge(e,r-1,5),Ge(e,n-4,4),i=0;i<n;i++)Ge(e,e.bl_tree[YE[i]*2+1],3);sE(e,e.dyn_ltree,t-1),sE(e,e.dyn_dtree,r-1)},uU=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<Vo;r++)if(e.dyn_ltree[r*2]!==0)return 1;return 0},lE=!1,sU=e=>{lE||(iU(),lE=!0),e.l_desc=new rp(e.dyn_ltree,XE),e.d_desc=new rp(e.dyn_dtree,ZE),e.bl_desc=new rp(e.bl_tree,KE),e.bi_buf=0,e.bi_valid=0,tM(e)},nM=(e,t,r,n)=>{Ge(e,(XV<<1)+(n?1:0),3),rM(e),Do(e,r),Do(e,~r),r&&e.pending_buf.set(e.window.subarray(t,t+r),e.pending),e.pending+=r},lU=e=>{Ge(e,VE<<1,3),zt(e,Mp,fr),rU(e)},cU=(e,t,r,n)=>{let i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=uU(e)),mp(e,e.l_desc),mp(e,e.d_desc),a=oU(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?nM(e,t,r,n):e.strategy===4||o===i?(Ge(e,(VE<<1)+(n?1:0),3),aE(e,fr,Co)):(Ge(e,(ZV<<1)+(n?1:0),3),aU(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),aE(e,e.dyn_ltree,e.dyn_dtree)),tM(e),n&&rM(e)},fU=(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[(Fo[r]+Vo+1)*2]++,e.dyn_dtree[JE(t)*2]++),e.sym_next===e.sym_end),dU=sU,hU=nM,pU=cU,mU=fU,vU=lU,_U={_tr_init:dU,_tr_stored_block:hU,_tr_flush_block:pU,_tr_tally:mU,_tr_align:vU},bU=(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},No=bU,gU=()=>{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},yU=new Uint32Array(gU()),wU=(e,t,r,n)=>{let i=yU,o=n+r;e^=-1;for(let a=n;a<o;a++)e=e>>>8^i[(e^t[a])&255];return e^-1},ye=wU,gn={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"},Mi={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:SU,_tr_stored_block:vp,_tr_flush_block:xU,_tr_tally:Ur,_tr_align:EU}=_U,{Z_NO_FLUSH:Wr,Z_PARTIAL_FLUSH:MU,Z_FULL_FLUSH:OU,Z_FINISH:dt,Z_BLOCK:cE,Z_OK:Ae,Z_STREAM_END:fE,Z_STREAM_ERROR:Ht,Z_DATA_ERROR:AU,Z_BUF_ERROR:ip,Z_DEFAULT_COMPRESSION:PU,Z_FILTERED:qU,Z_HUFFMAN_ONLY:Ec,Z_RLE:kU,Z_FIXED:TU,Z_DEFAULT_STRATEGY:CU,Z_UNKNOWN:jU,Z_DEFLATED:jc}=Mi,IU=9,LU=15,RU=8,FU=29,DU=256,_p=DU+1+FU,NU=30,BU=19,zU=2*_p+1,HU=15,W=3,Vr=258,Vt=Vr+W+1,VU=32,Si=42,Ap=57,bp=69,gp=73,yp=91,wp=103,_n=113,ko=666,Be=1,Oi=2,yn=3,Ai=4,UU=3,bn=(e,t)=>(e.msg=gn[t],t),dE=e=>e*2-(e>4?9:0),Hr=e=>{let t=e.length;for(;--t>=0;)e[t]=0},WU=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)},GU=(e,t,r)=>(t<<e.hash_shift^r)&e.hash_mask,Gr=GU,rt=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))},nt=(e,t)=>{xU(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,rt(e.strm)},Y=(e,t)=>{e.pending_buf[e.pending++]=t},qo=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=t&255},Sp=(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=No(e.adler,t,i,r):e.state.wrap===2&&(e.adler=ye(e.adler,t,i,r)),e.next_in+=i,e.total_in+=i,i)},iM=(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+Vr,h=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]!==h||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=Vr-(c-n),n=c-Vr,o>a){if(e.match_start=t,a=o,o>=u)break;h=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),WU(e),n+=t),e.strm.avail_in===0)break;if(r=Sp(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=W)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=Gr(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=Gr(e,e.ins_h,e.window[i+W-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<W)););}while(e.lookahead<Vt&&e.strm.avail_in!==0)},oM=(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===Wr||n!==i+e.strm.avail_in)))break;a=t===dt&&n===i+e.strm.avail_in?1:0,vp(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,rt(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&&(Sp(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 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up:if(r.last){l>>>=d&7,d-=d&7,r.mode=lp;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=PE;break;case 1:if(QW(r),r.mode=Ac,t===Oc){l>>>=2,d-=2;break e}break;case 2:r.mode=kE;break;case 3:e.msg="invalid block type",r.mode=oe}l>>>=2,d-=2;break;case PE: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=oe;break}if(r.length=l&65535,l=0,d=0,r.mode=sp,t===Oc)break e;case sp:r.mode=qE;case qE:if(h=r.length,h){if(h>u&&(h=u),h>f&&(h=f),h===0)break e;i.set(n.subarray(o,o+h),a),u-=h,o+=h,f-=h,a+=h,r.length-=h;break}r.mode=cr;break;case kE: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=oe;break}r.have=0,r.mode=TE;case TE:for(;r.have<r.ncode;){for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.lens[L[r.have++]]=l&7,l>>>=3,d-=3}for(;r.have<19;)r.lens[L[r.have++]]=0;if(r.lencode=r.lendyn,r.lenbits=7,P={bits:r.lenbits},q=Io(HW,r.lens,0,19,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid code lengths set",r.mode=oe;break}r.have=0,r.mode=CE;case CE:for(;r.have<r.nlen+r.ndist;){for(;p=r.lencode[l&(1<<r.lenbits)-1],_=p>>>24,y=p>>>16&255,w=p&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=oe;break}O=r.lens[r.have-1],h=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-=_,O=0,h=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-=_,O=0,h=11+(l&127),l>>>=7,d-=7}if(r.have+h>r.nlen+r.ndist){e.msg="invalid bit length repeat",r.mode=oe;break}for(;h--;)r.lens[r.have++]=O}}if(r.mode===oe)break;if(r.lens[256]===0){e.msg="invalid code -- missing end-of-block",r.mode=oe;break}if(r.lenbits=9,P={bits:r.lenbits},q=Io(dM,r.lens,0,r.nlen,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid literal/lengths set",r.mode=oe;break}if(r.distbits=6,r.distcode=r.distdyn,P={bits:r.distbits},q=Io(hM,r.lens,r.nlen,r.ndist,r.distcode,0,r.work,P),r.distbits=P.bits,q){e.msg="invalid distances set",r.mode=oe;break}if(r.mode=Ac,t===Oc)break e;case Ac:r.mode=Pc;case Pc:if(u>=6&&f>=258){e.next_out=a,e.avail_out=f,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,RW(e,c),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,r.mode===cr&&(r.back=-1);break}for(r.back=0;p=r.lencode[l&(1<<r.lenbits)-1],_=p>>>24,y=p>>>16&255,w=p&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(y&&!(y&240)){for(x=_,E=y,M=w;p=r.lencode[M+((l&(1<<x+E)-1)>>x)],_=p>>>24,y=p>>>16&255,w=p&65535,!(x+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=x,d-=x,r.back+=x}if(l>>>=_,d-=_,r.back+=_,r.length=w,y===0){r.mode=FE;break}if(y&32){r.back=-1,r.mode=cr;break}if(y&64){e.msg="invalid literal/length code",r.mode=oe;break}r.extra=y&15,r.mode=jE;case jE: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=IE;case IE:for(;p=r.distcode[l&(1<<r.distbits)-1],_=p>>>24,y=p>>>16&255,w=p&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(!(y&240)){for(x=_,E=y,M=w;p=r.distcode[M+((l&(1<<x+E)-1)>>x)],_=p>>>24,y=p>>>16&255,w=p&65535,!(x+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=x,d-=x,r.back+=x}if(l>>>=_,d-=_,r.back+=_,y&64){e.msg="invalid distance code",r.mode=oe;break}r.offset=w,r.extra=y&15,r.mode=LE;case 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Con ${o.length} seq ${i[0].seq.length}`);return{consensus:o,alns:i,header:r}}Wt.parseClustalIter=HM;function VM(e){let t=(0,IG.parsePairwiseBlocks)(e.split(`
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49
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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}}Wt.parsePairwiseIter=VM;function LG(e){let t=e.split(`
|
|
50
|
+
`)[Symbol.iterator]();return HM(t)}Wt.parse=LG;function RG(e){let t=e.split(`
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51
51
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`).filter(r=>!r.startsWith("#")).join(`
|
|
52
|
-
`);return
|
|
53
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i=0;i<10;i++)await Oc(1e3),e(`Re-checking MSA status in... ${10-i}`);if(await Me(`${rt}/${r}/status/${t}`)==="FINISHED")break}}async function nO({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return eU({sequence:t,onProgress:r});case"muscle":return tU({sequence:t,onProgress:r});case"kalign":return rU({sequence:t,onProgress:r});case"mafft":return nU({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}lh();function oO(e){return`${e.accession}-${e.sciname.replaceAll(" ","_")}`}function aO(e){return e.replace("-","")}async function uO({self:e}){let{blastDatabase:t,blastProgram:r,msaAlgorithm:n,proteinSequence:i}=e.blastParams,o=i.replaceAll("*","").replaceAll("&",""),{hits:a}=await iO({query:o,blastDatabase:t,blastProgram:r,onProgress:l=>e.setProgress(l),onRid:l=>e.setRid(l)}),u=[`>QUERY
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`);return VM(t)}Wt.parsePairwise=RG});var WM,$o,GM=C(()=>{WM=S(UM()),$o=class{MSA;constructor(t){this.MSA=(0,WM.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 Yo(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=Number.parseFloat(o))}}}return r}var Dp=C(()=>{});var $M,Xo,YM=C(()=>{$M=S(Kh());Dp();Br();Xo=class{data;MSA;constructor(t,r){let n=$M.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 ${r+1}`)}getHeader(){return{General:this.MSA.gf,Accessions:this.MSA.gs?.AC,Dbxref:this.MSA.gs?.DR}}getRowData(t){return{name:t,accession:this.MSA.gs?.AC?.[t],dbxref:this.MSA.gs?.DR?.[t]}}getNames(){return Object.keys(this.MSA.seqdata)}getSeqCoords(){}getStructures(){let t=/PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/,r=this.MSA,n=Object.entries(r.gs?.DR||{}).map(([o,a])=>[o,t.exec(a)]).filter(o=>!!o[1]).map(([o,a])=>{let u=a[1].toLowerCase(),f=a[2],l=+a[3],d=+a[4];return{id:o,pdb:u,chain:f,startPos:l,endPos:d}}),i={};for(let o of n){let{id:a,...u}=o;i[a]||(i[a]=[]),i[a].push(u)}return i}getTree(){let t=this.MSA?.gf?.NH?.[0];return t?yo(Yo(t)):{id:"root",name:"root",noTree:!0,branchset:this.getNames().map(r=>({id:r,branchset:[],name:r}))}}get seqConsensus(){return this.MSA.gc?.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc?.SS_cons}get tracks(){return[{id:"seqConsensus",name:"Sequence consensus",data:this.seqConsensus,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:this.secondaryStructureConsensus,customColorScheme:{">":"pink","<":"lightblue"}}]}}});function FG(e){return e.split(">").filter(t=>/\S/.test(t)).map(t=>{let[r,...n]=t.split(`
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t$({rid:e,progress:t}){let{classes:r}=UO();return pt.default.createElement("div",{className:r.loading},e?pt.default.createElement($p,{rid:e}):null,pt.default.createElement(Yp.Typography,null,t))}var pt,Yp,HO,VO,Yc,UO,r$,WO,GO=C(()=>{"use strict";pt=S(I()),Yp=S(z()),HO=S(N()),VO=S(Ot()),Yc=S(Se());zO();UO=(0,VO.makeStyles)()(e=>({margin:{padding:20},loading:{background:e.palette.background.paper}}));r$=(0,HO.observer)(function({model:t}){let{progress:r,rid:n,error:i,processing:o}=t,{classes:a}=UO();return pt.default.createElement("div",{className:a.margin},pt.default.createElement(Yc.LoadingEllipses,{message:"Running NCBI BLAST",variant:"h5"}),i?pt.default.createElement(e$,{rid:n,error:i}):n?pt.default.createElement(t$,{rid:n,progress:r}):null,pt.default.createElement(Yp.Typography,null,o||"Initializing BLAST query"))}),WO=r$});var YO={};at(YO,{default:()=>i$});var Xc,$O,n$,i$,XO=C(()=>{"use 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Bc({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Pe(`${it}/clustalo/result/${r}/aln-clustal_num`),tree:await Pe(`${it}/clustalo/result/${r}/phylotree`)}}async function $G({sequence:e,onProgress:t}){let r=await Pe(`${it}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await Bc({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Pe(`${it}/muscle/result/${r}/fa`),tree:await Pe(`${it}/muscle/result/${r}/phylotree`)}}async function YG({sequence:e,onProgress:t}){let r=await Pe(`${it}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Bc({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Pe(`${it}/kalign/result/${r}/fa`),tree:await Pe(`${it}/kalign/result/${r}/phylotree`)}}async function XG({sequence:e,onProgress:t}){let r=await Pe(`${it}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Bc({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Pe(`${it}/mafft/result/${r}/fa`),tree:await Pe(`${it}/mafft/result/${r}/phylotree`)}}async function Bc({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let i=0;i<10;i++)await Nc(1e3),e(`Re-checking MSA status in... ${10-i}`);if(await Pe(`${it}/${r}/status/${t}`)==="FINISHED")break}}async function PO({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return GG({sequence:t,onProgress:r});case"muscle":return $G({sequence:t,onProgress:r});case"kalign":return YG({sequence:t,onProgress:r});case"mafft":return XG({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}Up();function kO(e){return`${e.accession}-${e.sciname.replaceAll(" ","_")}`}function TO(e){return e.replace("-","")}async function CO({self:e}){let{blastDatabase:t,blastProgram:r,msaAlgorithm:n,proteinSequence:i}=e.blastParams,o=i.replaceAll("*","").replaceAll("&",""),{hits:a}=await qO({query:o,blastDatabase:t,blastProgram:r,onProgress:l=>e.setProgress(l),onRid:l=>e.setRid(l)}),u=[`>QUERY
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54
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+
${o}`,...a.map(l=>[kO(l.description[0]),TO(l.hsps[0].hseq)]).map(([l,d])=>`>${l}
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55
55
|
${d}`)].join(`
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56
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-
`);return await
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57
|
-
${
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58
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-
`).map(r=>r.trim()).filter(r=>!!r)}function Ei(e){let t=e.length;for(;--t>=0;)e[t]=0}var EU=0,qM=1,OU=2,MU=3,AU=258,Vh=29,Zo=256,Ho=Zo+1+Vh,wi=30,Uh=19,kM=2*Ho+1,hn=15,yh=16,PU=7,Wh=256,TM=16,CM=17,jM=18,Ih=new Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]),Hc=new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),qU=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),IM=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),kU=512,lr=new Array((Ho+2)*2);Ei(lr);var No=new Array(wi*2);Ei(No);var Vo=new Array(kU);Ei(Vo);var Uo=new Array(AU-MU+1);Ei(Uo);var Gh=new Array(Vh);Ei(Gh);var Vc=new Array(wi);Ei(Vc);function wh(e,t,r,n,i){this.static_tree=e,this.extra_bits=t,this.extra_base=r,this.elems=n,this.max_length=i,this.has_stree=e&&e.length}var RM,LM,FM;function Sh(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}var DM=e=>e<256?Vo[e]:Vo[256+(e>>>7)],Wo=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},$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],$e(e,n,u)));while(o<e.sym_next);zt(e,Wh,t)},Rh=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,f=-1,l;for(e.heap_len=0,e.heap_max=kM,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=f=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=f<2?++f:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=f,a=e.heap_len>>1;a>=1;a--)xh(e,r,a);l=o;do 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i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=LU(e)),Rh(e,e.l_desc),Rh(e,e.d_desc),a=IU(e),i=e.opt_len+3+7>>>3,o=e.static_len+3+7>>>3,o<=i&&(i=o)):i=o=r+5,r+4<=i&&t!==-1?VM(e,t,r,n):e.strategy===4||o===i?($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=$U,YU=()=>{let e,t=[];for(var r=0;r<256;r++){e=r;for(var 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version"},Oi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8},{_tr_init:KU,_tr_stored_block:Lh,_tr_flush_block:JU,_tr_tally:Hr,_tr_align:QU}=GU,{Z_NO_FLUSH:Vr,Z_PARTIAL_FLUSH:eW,Z_FULL_FLUSH:tW,Z_FINISH:dt,Z_BLOCK:ZO,Z_OK:Pe,Z_STREAM_END:KO,Z_STREAM_ERROR:Ht,Z_DATA_ERROR:rW,Z_BUF_ERROR:Eh,Z_DEFAULT_COMPRESSION:nW,Z_FILTERED:iW,Z_HUFFMAN_ONLY:Fc,Z_RLE:oW,Z_FIXED:aW,Z_DEFAULT_STRATEGY:uW,Z_UNKNOWN:sW,Z_DEFLATED:Gc}=Oi,lW=9,cW=15,fW=8,dW=29,pW=256,Fh=pW+1+dW,hW=30,mW=19,vW=2*Fh+1,_W=15,V=3,zr=258,Vt=zr+V+1,bW=32,Si=42,$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 De;if(e.lookahead===0)break}if(e.match_length=0,e.lookahead>=V&&e.strstart>0&&(i=e.strstart-1,n=a[i],n===a[++i]&&n===a[++i]&&n===a[++i])){o=e.strstart+zr;do;while(n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&i<o);e.match_length=zr-(o-i),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=V?(r=Hr(e,1,e.match_length-V),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(r=Hr(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),r&&(ot(e,!1),e.strm.avail_out===0))return De}return e.insert=0,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},xW=(e,t)=>{let r;for(;;){if(e.lookahead===0&&(xi(e),e.lookahead===0)){if(t===Vr)return De;break}if(e.match_length=0,r=Hr(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++,r&&(ot(e,!1),e.strm.avail_out===0))return De}return e.insert=0,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};function Bt(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 Do=[new Bt(0,0,0,0,WM),new Bt(4,4,8,4,Oh),new Bt(4,5,16,8,Oh),new Bt(4,6,32,32,Oh),new Bt(4,4,16,16,gi),new Bt(8,16,32,32,gi),new Bt(8,16,128,128,gi),new Bt(8,32,128,256,gi),new Bt(32,128,258,1024,gi),new Bt(32,258,258,4096,gi)],EW=e=>{e.window_size=2*e.w_size,Br(e.head),e.max_lazy_match=Do[e.level].max_lazy,e.good_match=Do[e.level].good_length,e.nice_match=Do[e.level].nice_length,e.max_chain_length=Do[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 OW(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=Gc,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(vW*2),this.dyn_dtree=new Uint16Array((2*hW+1)*2),this.bl_tree=new Uint16Array((2*mW+1)*2),Br(this.dyn_ltree),Br(this.dyn_dtree),Br(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(_W+1),this.heap=new 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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 repeat",r.mode=ne;break}for(;p--;)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=zo(JM,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=zo(QM,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=Bc,t===Nc)break e;case Bc:r.mode=zc;case zc:if(u>=6&&f>=258){e.next_out=a,e.avail_out=f,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,fG(e,c),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,r.mode===sr&&(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,O=w;h=r.lencode[O+((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=xM;break}if(y&32){r.back=-1,r.mode=sr;break}if(y&64){e.msg="invalid literal/length code",r.mode=ne;break}r.extra=y&15,r.mode=gM;case gM: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=yM;case yM: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,O=w;h=r.distcode[O+((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=wM;case 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M2.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=cm}install(r){hh(r),Kh(r),tm(r)}configure(r){(0,A2.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:P2.default,onClick:n=>{n.addView("MsaView",{})}})}};return I2(p$);})();
|
|
56
|
+
`);return await PO({algorithm:n,sequence:u,onProgress:l=>e.setProgress(l)})}var IO=S(we());function jO(e){return!!e&&typeof e=="object"&&"hoverFeature"in e&&"hoverPosition"in e}function LO({model:e}){let{hovered:t}=(0,IO.getSession)(e),{transcriptToMsaMap:r,connectedView:n}=e;if(n?.initialized&&r&&jO(t)){let{coord:i}=t.hoverPosition,{g2p:o}=r,a=o[i];if(a!==void 0)return e.seqCoordToRowSpecificGlobalCoord("QUERY",a+1)}}function zc({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 DO=S(RO());function Wp(){return _e.types.compose(FO.BaseViewModel,zp(),_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,DO.genomeToTranscriptSeqMapping)(e.connectedFeature):void 0}})).views(e=>({get mouseCol2(){return LO({model:e})},get clickCol2(){}})).views(e=>({get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Uc.getSession)(e);return 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${p}`:"Loading...",InputProps:{readOnly:!0,classes:{input:i.textAreaFont}}}),qe.default.createElement(Et.DialogActions,null,qe.default.createElement(Et.Button,{color:"primary",variant:"contained",onClick:()=>{c2({feature:h,view:o,newViewTitle:`NCBI BLAST - ${Qo(r)} - ${Mn(h)} - ${f}`}).setBlastParams({blastProgram:"blastp",blastDatabase:a,msaAlgorithm:f,selectedTranscript:h,proteinSequence:p}),t()},disabled:!p},"Submit"),qe.default.createElement(Et.Button,{color:"secondary",variant:"contained",onClick:()=>t()},"Cancel")))}),em=m$;var me=S(I()),_2=S(N()),b2=S(Se()),Ye=S(z()),Kc=S(we()),g2=S(Ot());async function m2(){let e=await fetch("https://jbrowse.org/demos/msaview/knownCanonical/list.txt");if(!e.ok)throw new Error(`HTTP ${e.status} fetching list ${await e.text()}`);return(await e.text()).split(`
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`).map(r=>r.trim()).filter(r=>!!r)}kp();async function v$(e){let t=await fetch(e);if(!t.ok)throw new Error(`HTTP ${t.status} fetching ${await t.text()}`);let r=await t.arrayBuffer();return new TextDecoder().decode(Rc(r))}async function v2({userSelection:e,session:t,newViewTitle:r,view:n,feature:i}){let o=await v$(`https://jbrowse.org/demos/msaview/knownCanonical/${e}.mfa.gz`);t.addView("MsaView",{type:"MsaView",displayName:r,treeAreaWidth:200,treeWidth:100,drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",treeFilehandle:{uri:"https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh"},treeMetadataFilehandle:{uri:"https://s3.amazonaws.com/jbrowse.org/demos/app/species.json"},data:{msa:o},connectedViewId:n.id,connectedFeature:i.toJSON()})}var _$=(0,g2.makeStyles)()({dialogContent:{width:"80em"}}),b$=(0,_2.observer)(function({model:t,feature:r,handleClose:n}){let 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ra.default.createElement(ra.default.Fragment,null,ra.default.createElement(O2,{model:t}),ra.default.createElement(A2,{model:t}))}),q2=M$;function am(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t=[],{model:r})=>[...t,k2.default.createElement(q2,{key:"highlight_protein_viewer_msaview",model:r})])}var tf=class extends T2.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=mm}install(r){Xp(r),rm(r),am(r)}configure(r){(0,C2.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:j2.default,onClick:n=>{n.addView("MsaView",{})}})}};return N2(O$);})();
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