jbrowse-plugin-msaview 5.2.0 → 5.3.0

package/dist/chunks/{TreeNodeInfoDialog-VRCVIF26.js.map → TreeNodeInfoDialog-T5XMPG3R.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport MetadataTable from '../../MetadataTable.tsx'\nimport SequenceTextArea from '../../SequenceTextArea.tsx'\n\nimport type { MsaViewModel } from '../../../model.ts'\n\nconst TreeNodeInfoDialog = observer(function ({\n  info,\n  model,\n  nodeName,\n  onClose,\n}: {\n  info: Record<string, unknown>\n  model: MsaViewModel\n  nodeName: string\n  onClose: () => void\n}) {\n  const { rows } = model\n  const metadata = model.rowDataOf(nodeName)\n  const res = rows.find(f => f[0] === nodeName)\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Tree node info\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <Typography variant=\"h6\">Attributes</Typography>\n        <MetadataTable record={{ nodeName, ...info }} />\n        <Typography variant=\"h6\">Sequence</Typography>\n        {res ? (\n          <SequenceTextArea str={[res]} />\n        ) : (\n          <Typography>Sequence not found</Typography>\n        )}\n        {metadata ? (\n          <>\n            <Typography variant=\"h6\">Extra metadata</Typography>\n            <MetadataTable record={metadata} />\n          </>\n        ) : null}\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default TreeNodeInfoDialog\n"],
-  "mappings": "0ZAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAA0C,SAC1CC,EAAyB,SAOzB,IAAMC,KAAqB,YAAS,SAAU,CAC5C,KAAAC,EACA,MAAAC,EACA,SAAAC,EACA,QAAAC,CAAO,EAMR,CACC,GAAM,CAAE,KAAAC,CAAI,EAAKH,EACXI,EAAWJ,EAAM,UAAUC,CAAQ,EACnCI,EAAMF,EAAK,KAAKG,GAAKA,EAAE,CAAC,IAAML,CAAQ,EAC5C,OACE,EAAAM,QAAA,cAAC,SAAM,CACL,QAAS,IAAK,CACZL,EAAO,CACT,EACA,KAAI,GACJ,MAAM,iBACN,SAAS,IAAI,EAEb,EAAAK,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,YAAA,EACxB,EAAAA,QAAA,cAACC,EAAa,CAAC,OAAQ,CAAE,SAAAP,EAAU,GAAGF,CAAI,CAAE,CAAA,EAC5C,EAAAQ,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,UAAA,EACvBF,EACC,EAAAE,QAAA,cAACE,EAAgB,CAAC,IAAK,CAACJ,CAAG,CAAC,CAAA,EAE5B,EAAAE,QAAA,cAAC,aAAU,KAAA,oBAAA,EAEZH,EACC,EAAAG,QAAA,cAAA,EAAAA,QAAA,SAAA,KACE,EAAAA,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,gBAAA,EACxB,EAAAA,QAAA,cAACC,EAAa,CAAC,OAAQJ,CAAQ,CAAA,CAAI,EAEnC,IAAI,CACM,CAGtB,CAAC,EAEDM,EAAeZ",
+  "mappings": "sbAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAA0C,SAC1CC,EAAyB,SAOzB,IAAMC,KAAqB,YAAS,SAAU,CAC5C,KAAAC,EACA,MAAAC,EACA,SAAAC,EACA,QAAAC,CAAO,EAMR,CACC,GAAM,CAAE,KAAAC,CAAI,EAAKH,EACXI,EAAWJ,EAAM,UAAUC,CAAQ,EACnCI,EAAMF,EAAK,KAAKG,GAAKA,EAAE,CAAC,IAAML,CAAQ,EAC5C,OACE,EAAAM,QAAA,cAAC,SAAM,CACL,QAAS,IAAK,CACZL,EAAO,CACT,EACA,KAAI,GACJ,MAAM,iBACN,SAAS,IAAI,EAEb,EAAAK,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,YAAA,EACxB,EAAAA,QAAA,cAACC,EAAa,CAAC,OAAQ,CAAE,SAAAP,EAAU,GAAGF,CAAI,CAAE,CAAA,EAC5C,EAAAQ,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,UAAA,EACvBF,EACC,EAAAE,QAAA,cAACE,EAAgB,CAAC,IAAK,CAACJ,CAAG,CAAC,CAAA,EAE5B,EAAAE,QAAA,cAAC,aAAU,KAAA,oBAAA,EAEZH,EACC,EAAAG,QAAA,cAAA,EAAAA,QAAA,SAAA,KACE,EAAAA,QAAA,cAAC,aAAU,CAAC,QAAQ,IAAI,EAAA,gBAAA,EACxB,EAAAA,QAAA,cAACC,EAAa,CAAC,OAAQJ,CAAQ,CAAA,CAAI,EAEnC,IAAI,CACM,CAGtB,CAAC,EAEDM,EAAeZ",
   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "TreeNodeInfoDialog", "info", "model", "nodeName", "onClose", "rows", "metadata", "res", "f", "React", "MetadataTable", "SequenceTextArea", "TreeNodeInfoDialog_default"]
 }

package/dist/chunks/chunk-6EOYBBT4.js

@@ -0,0 +1,2 @@
+var o="9.1.0";export{o as a};
+//# sourceMappingURL=chunk-6EOYBBT4.js.map

package/dist/chunks/chunk-6EOYBBT4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/version.ts"],
+  "sourcesContent": ["export const version = '9.1.0'\n"],
+  "mappings": "AAAO,IAAMA,EAAU",
+  "names": ["version"]
+}

package/dist/chunks/chunk-A63PUWQZ.js

@@ -0,0 +1,6 @@
+import{a as O,b as $}from"./chunk-K55ZVN73.js";import{a as _}from"./chunk-73KAPCJ2.js";import{a as J}from"./chunk-J6KYLXRD.js";import{b as z}from"./chunk-FY3BTKY4.js";function V(e){try{return new URL(e).host}catch{return e}}var R=class extends Error{constructor(r,n){super(r);this.status=n}};async function P(e,t){let r;try{r=await fetch(e,t)}catch(n){throw n instanceof TypeError?new Error(`Could not reach ${V(e)} \u2014 the request failed at the network level. This is usually a CORS restriction (the server refused to let this site read the response), an offline connection, or a blocked request.`,{cause:n}):n}if(!r.ok)throw new R(`HTTP ${r.status} fetching ${e} ${(await r.text()).slice(0,500)}`,r.status);return r}async function A(e,t){return(await P(e,t)).text()}async function Nt(e,t){return(await P(e,t)).json()}function N(e,t){return new Promise((r,n)=>{if(t?.aborted){n(new DOMException("Aborted","AbortError"));return}let s=()=>{clearTimeout(o),n(new DOMException("Aborted","AbortError"))},o=setTimeout(()=>{t?.removeEventListener("abort",s),r()},e);t?.addEventListener("abort",s,{once:!0})})}function k(e){return e instanceof Error&&e.name==="AbortError"}var D=z(J());function T(e,t){try{let r=globalThis.localStorage.getItem(e);return r===null?t:JSON.parse(r)}catch(r){return console.error(r),t}}function Dt(e,t){let[r,n]=(0,D.useState)(()=>T(e,t));return[r,o=>{n(o);try{globalThis.localStorage.setItem(e,JSON.stringify(o))}catch(a){console.error(a)}}]}async function q({check:e,intervalSeconds:t,onCountdown:r,signal:n}){for(;;){if(n?.throwIfAborted(),await e())return;for(let s=t;s>0;s--)r(s),await N(1e3,n)}}var M="https://www.ebi.ac.uk/Tools/services/rest",X="msa-ebiContactEmail",I="jbrowse2@berkeley.edu";function Y(){return T(X,I).trim()||I}var Q=new Set(["ERROR","FAILURE","NOT_FOUND"]);async function Z({tool:e,params:t,signal:r}){return(await A(`${M}/${e}/run`,{method:"POST",body:new URLSearchParams({email:Y(),...t}),signal:r})).trim()}var L=900*1e3;async function tt({tool:e,jobId:t,intervalSeconds:r=10,onCountdown:n,signal:s}){let o;await q({intervalSeconds:r,onCountdown:n,signal:s,check:async()=>{let a;try{a=(await A(`${M}/${e}/status/${t}`,{signal:s})).trim()}catch(i){if(k(i))throw i;if(o??=Date.now(),Date.now()-o>=L)throw new Error(`Could not reach EBI to check ${e} job ${t} for ${Math.round(L/6e4)} minutes`,{cause:i});return console.warn("[msaview] EBI status check failed, retrying:",i),!1}if(o=void 0,a==="FINISHED")return!0;if(Q.has(a))throw new Error(`EBI ${e} job ${t} returned status ${a}`);return!1}})}async function Gt({tool:e,label:t,params:r,onProgress:n,onRid:s,signal:o}){n(`Submitting ${t} to EBI...`);let a=await Z({tool:e,params:r,signal:o});return s?.(a),await tt({tool:e,jobId:a,signal:o,onCountdown:i=>{n(`Re-checking ${t} status in... ${i}`)}}),{jobId:a,result:i=>A(`${M}/${e}/result/${a}/${i}`,{signal:o})}}var Ht="https://blast.ncbi.nlm.nih.gov/Blast.cgi",et=["clustalo","muscle","kalign","mafft"],Kt=[...et,"browser"],Wt={clustalo:"Clustal Omega (EBI)",muscle:"MUSCLE (EBI)",kalign:"Kalign (EBI)",mafft:"MAFFT (EBI)",browser:"in browser, query-anchored"},rt=["uniprotkb_swissprot","uniprotkb","pan_proteomes","uniprotkb_trembl"],nt="uniprotkb_swissprot",zt=["blastp","phmmer"],Jt={blastp:"blastp (sequence search)",phmmer:"phmmer (profile HMM search)"},st=["swissprot","uniprotkb","uniprotrefprot","rp75","rp55","rp35","rp15"],ot="swissprot",B=[5,10,20,50,100,150,200,250,500,750,1e3],Vt=100;function Xt(e){return B.find(t=>t>=e)??B.at(-1)}function Yt(e){return e==="phmmer"?{program:e,database:ot}:{program:e,database:nt}}function Qt(e){return e==="phmmer"?st:rt}var it={uniprotkb_swissprot:"UniProtKB/Swiss-Prot (curated)",swissprot:"UniProtKB/Swiss-Prot (curated)",uniprotkb:"UniProtKB (all entries)",uniprotkb_trembl:"UniProtKB/TrEMBL (unreviewed)",pan_proteomes:"Pan-proteomes",uniprotrefprot:"UniProt reference proteomes",rp75:"Representative proteomes, 75%",rp55:"Representative proteomes, 55%",rp35:"Representative proteomes, 35%",rp15:"Representative proteomes, 15% (widest spread)"};function Zt(e){return it[e]}function y(e,t="node",r=0){let n=(a,i)=>({...a,id:i,name:a.name||i,children:[]}),s=n(e,`${t}-${r}`),o=[{src:e,out:s,depth:r}];for(;o.length>0;){let{src:a,out:i,depth:c}=o.pop();if(a.children){i.children=a.children.map((u,f)=>n(u,`${i.id}-${f}-${c+1}`));for(let[u,f]of a.children.entries())o.push({src:f,out:i.children[u],depth:c+1})}}return s}var p=class{rows=new Map;names;width;constructor(t){for(let[r,n]of t)this.rows.has(r)||this.rows.set(r,n);this.names=[...this.rows.keys()]}getRow(t){return this.rows.get(t)??""}getNames(){return this.names}getWidth(){return this.width??=this.getNames().reduce((t,r)=>Math.max(t,this.getRow(r).length),0),this.width}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,children:[],name:t}))}}getRowData(t){}getStructures(){return{}}getHeader(){return{}}get alignmentNames(){return[]}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}};function S(e){return _(e,{postParenNumeric:"name"})}function j(){return{gf:Object.create(null),gc:Object.create(null),gs:Object.create(null),gr:Object.create(null),seqname:[],seqdata:Object.create(null)}}function b(e,t){if(e)return e;if(t)throw new Error("No format header: # STOCKHOLM 1.0");return j()}var U=/^# STOCKHOLM 1.0/,at=/^\/\/\s*$/,ct=/^#=GF\s+(\S+)\s+(.*?)\s*$/,ut=/^#=GC\s+(\S+)\s+(.*?)\s*$/,pt=/^#=GS\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,ft=/^#=GR\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,lt=/^\s*([^#\s]\S*)\s+(\S+)\s*$/,mt=/\S/;function x(e){return U.test(e)}function G(e,t){let r=t??{},n=[],s=null,o=!1,a=e.split(`
+`);for(let i of a){let c;if(U.test(i))s&&n.push(s),s=j(),o=!1;else if(at.test(i))s&&n.push(s),s=null;else if(c=ct.exec(i)){s=b(s,!!r.strict);let u=c[1],f=s.gf[u]??=[];u==="NH"&&o&&f.length>0?f[f.length-1]+=c[2]:f.push(c[2]),o=u==="NH"}else if(c=ut.exec(i))s=b(s,!!r.strict),s.gc[c[1]]=(s.gc[c[1]]??"")+c[2];else if(c=pt.exec(i)){s=b(s,!!r.strict);let u=s.gs[c[2]]??=Object.create(null);(u[c[1]]??=[]).push(c[3])}else if(c=ft.exec(i)){s=b(s,!!r.strict);let u=s.gr[c[2]]??=Object.create(null);u[c[1]]=(u[c[1]]??"")+c[3]}else if(c=lt.exec(i)){s=b(s,!!r.strict);let u=c[1],f=c[2];s.seqdata[u]===void 0&&(s.seqdata[u]="",s.seqname.push(u)),s.seqdata[u]+=f}else if(mt.test(i)&&r.strict)throw new Error("Malformed line")}return s&&n.push(s),n}var m=class extends p{data;MSA;constructor(t,r){let n=G(t),s=n[r]??n[0];if(!s)throw new Error("No alignments found in Stockholm file");super(s.seqname.map(o=>[o,s.seqdata[o]??""])),this.data=n,this.MSA=s}getMSA(){return this.MSA}get alignmentNames(){return this.data.map((t,r)=>t.gf.DE?.[0]??`Alignment ${r+1}`)}getHeader(){let t=this.MSA.gs.AC??{},r=this.MSA.gs.DR??{};return{General:this.MSA.gf,Accessions:Object.fromEntries(Object.entries(t).map(([n,s])=>[n,s[0]])),Dbxref:Object.fromEntries(Object.entries(r).map(([n,s])=>[n,s.join("; ")]))}}getRowData(t){return{name:t,accession:this.MSA.gs.AC?.[t]?.[0],dbxref:this.MSA.gs.DR?.[t]?.join("; ")}}getStructures(){let t=/PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/,r=this.MSA.gs.DR??{},n={};for(let[s,o]of Object.entries(r))for(let a of o){let i=t.exec(a);i&&(n[s]??=[]).push({pdb:i[1].toLowerCase(),chain:i[2],startPos:+i[3],endPos:+i[4]})}return n}getTree(){let t=this.MSA.gf.NH?.[0];return t?y(S(t)):super.getTree()}get seqConsensus(){return this.MSA.gc.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc.SS_cons}get tracks(){let{seq_cons:t,SS_cons:r,...n}=this.MSA.gc;return[{id:"seqConsensus",name:"Sequence consensus",data:t,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:r,customColorScheme:H},...Object.entries(n).map(([s,o])=>({id:`gc-${s}`,name:s,data:o,customColorScheme:v(s)})),...Object.entries(this.MSA.gr).flatMap(([s,o])=>Object.entries(o).map(([a,i])=>({id:`gr-${a}-${s}`,name:`${a} ${s}`,data:i,customColorScheme:v(s),defaultOff:!0})))]}},H={"<":"lightblue","(":"lightblue","[":"lightblue","{":"lightblue",">":"pink",")":"pink","]":"pink","}":"pink"};function v(e){return e==="SS"||e.endsWith("_SS")?H:{}}function E(e){return/^(#.*\n)*>/.test(e)}function C(e){let t=[],r=new Set,n,s=()=>{n&&!r.has(n.id)&&(r.add(n.id),t.push({id:n.id,seq:n.lines.join("").replaceAll(/\s/g,"")}))},o=0;for(let a of e.split(`
+`))a.startsWith(">")?(s(),o++,n={id:/^>\s*(\S*)/.exec(a)[1]||`unnamed_${o}`,lines:[]}):n?.lines.push(a);return s(),t}function w(e){return typeof e=="string"?C(e):e}var dt=65,ht=90,gt=97,St=122,bt=45;function K(e){return e>=gt&&e<=St}function W(e){return e>=dt&&e<=ht||e===bt}function xt(e){let t=[],r=[""];for(let n of e){let s=n.charCodeAt(0);W(s)?(t.push(n),r.push("")):K(s)&&(r[r.length-1]+=n.toUpperCase())}return{matches:t,inserts:r}}var l=class extends p{constructor(t){let r=w(t),n=wt(r.map(s=>s.seq));super(r.map((s,o)=>[s.id,n[o]]))}static sniff(t){if(typeof t=="string"&&!E(t))return!1;let r=w(t).map(o=>o.seq).filter(o=>!!o);if(r.length<2||new Set(r.map(o=>o.length)).size===1)return!1;let n=!1,s;for(let o of r){let a=0;for(let i=0;i<o.length;i++){let c=o.charCodeAt(i);W(c)?a++:K(c)&&(n=!0)}if(s!==void 0&&a!==s)return!1;s=a}return n}};function wt(e){let t=e.map(xt),r=0;for(let{matches:s}of t)r=Math.max(r,s.length);let n=new Array(r+1).fill(0);for(let{inserts:s}of t)for(let[o,a]of s.entries())n[o]=Math.max(n[o],a.length);return t.map(({matches:s,inserts:o})=>{let a=[];for(let i=0;i<=r;i++){let c=o[i]??"";a.push(c,".".repeat(n[i]-c.length)),i<r&&a.push(s[i]??"-")}return a.join("")})}var d=class extends p{MSA;constructor(t){let r=O(t);super(r.alns.map(n=>[n.id,n.seq])),this.MSA=r}getHeader(){return this.MSA.header}get seqConsensus(){return this.MSA.consensus}};var h=class extends p{constructor(t){super($(t).map(r=>[r.protein,r.seq]))}};var g=class extends p{colonNormalized=new Map;constructor(t){let r=w(t);super(r.map(n=>[n.id,n.seq]));for(let{id:n}of r)n.includes(":")&&this.colonNormalized.set(n.replaceAll(":","_"),n)}getRow(t){return this.rows.get(t)??this.rows.get(this.colonNormalized.get(t)??"")??""}};var Et=/^<(!doctype\s+html|html[\s>])/i,Rt=/^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i;function Tt(e,t=0,r){let n=e.replace(/^\uFEFF/,"").replaceAll(/\r\n?/g,`
+`).trimStart();if(Et.test(n))throw new Error("Received an HTML page, not an alignment. Check that the URL points at the file itself");if(r==="stockholm")return new m(n,t);if(r==="a3m")return new l(n);if(r==="fasta")return new g(n);if(r==="emf")return new h(n);if(r==="clustal")return new d(n);if(x(n))return new m(n,t);if(E(n)){let o=C(n);return l.sniff(o)?new l(o):new g(o)}if(n.startsWith("SEQ"))return new h(n);if(Rt.test(n))return new d(n);let s=n.split(`
+`,1)[0].slice(0,80);throw new Error(s?`Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads "${s}"`:"The alignment file is empty")}function Mt(e){return e.replaceAll(/[.-]/g,"")}export{R as a,P as b,A as c,Nt as d,N as e,k as f,Dt as g,X as h,I as i,Gt as j,Ht as k,Kt as l,Wt as m,zt as n,Jt as o,Vt as p,Xt as q,Yt as r,Qt as s,Zt as t,m as u,Tt as v,Mt as w};
+//# sourceMappingURL=chunk-A63PUWQZ.js.map

package/dist/chunks/chunk-A63PUWQZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/fetch.ts", "../../src/utils/useLocalStorage.ts", "../../src/utils/poll.ts", "../../src/utils/ebiJobDispatcher.ts", "../../src/LaunchMsaView/components/BlastQuery/consts.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/util.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/BaseMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/parseNewick.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/stockholmParser.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/StockholmMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/fastaRecords.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/A3mMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/ClustalMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/EmfMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/FastaMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.0.0/node_modules/msa-parsers/src/msa/index.ts"],
+  "sourcesContent": ["function hostOf(url: string) {\n  try {\n    return new URL(url).host\n  } catch {\n    // a relative url, e.g. a same-origin proxy path\n    return url\n  }\n}\n\nexport class HttpError extends Error {\n  constructor(\n    message: string,\n    readonly status: number,\n  ) {\n    super(message)\n  }\n}\n\nexport async function handleFetch(url: string, args?: RequestInit) {\n  let response: Response\n  try {\n    response = await fetch(url, args)\n  } catch (e) {\n    // fetch rejects with a bare \"TypeError: Failed to fetch\" for every network\n    // level failure, including a cross-origin response the browser refused to\n    // hand over. That is not a hypothetical: NCBI's Blast.cgi stopped sending\n    // Access-Control-Allow-Origin to third-party origins, and the raw TypeError\n    // told users nothing at all about why. See docs/blast.md.\n    if (e instanceof TypeError) {\n      throw new Error(\n        `Could not reach ${hostOf(url)} \u2014 the request failed at the network level. This is usually a CORS restriction (the server refused to let this site read the response), an offline connection, or a blocked request.`,\n        { cause: e },\n      )\n    }\n    throw e\n  }\n\n  if (!response.ok) {\n    throw new HttpError(\n      `HTTP ${response.status} fetching ${url} ${(await response.text()).slice(0, 500)}`,\n      response.status,\n    )\n  }\n\n  return response\n}\n\nexport async function textfetch(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.text()\n}\n\nexport async function jsonfetch<T>(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.json() as Promise<T>\n}\n\nexport function timeout(time: number, signal?: AbortSignal) {\n  return new Promise<void>((resolve, reject) => {\n    if (signal?.aborted) {\n      reject(new DOMException('Aborted', 'AbortError'))\n      return\n    }\n    // the listener is removed on the natural path too: one signal serves every\n    // tick of a poll, and a 10-minute job is ~600 sleeps -- leaving each\n    // listener behind accumulates them all on that one signal\n    const onAbort = () => {\n      clearTimeout(id)\n      reject(new DOMException('Aborted', 'AbortError'))\n    }\n    const id = setTimeout(() => {\n      signal?.removeEventListener('abort', onAbort)\n      resolve()\n    }, time)\n    signal?.addEventListener('abort', onAbort, { once: true })\n  })\n}\n\n/**\n * A cancelled launch has to be told apart from a failed one: it must not render\n * the \"failed\" panel, and it must not touch a model that may already be gone.\n * `fetch` and the sleep above both reject with a DOMException named AbortError,\n * which subclasses Error.\n */\nexport function isAbortError(e: unknown) {\n  return e instanceof Error && e.name === 'AbortError'\n}\n", "import { useState } from 'react'\n\n// Vendored rather than imported from `@jbrowse/core/util`: that barrel is\n// host-provided, and a barrel split dropped this export, making the BLAST panel\n// throw \"(0, PR.useLocalStorage) is not a function\" on hosts built during that\n// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes\n// this plugin out of the whack-a-mole.\nexport function readLocalStorage<T>(key: string, initialValue: T): T {\n  try {\n    const item = globalThis.localStorage.getItem(key)\n    return item === null ? initialValue : (JSON.parse(item) as T)\n  } catch (error) {\n    console.error(error)\n    return initialValue\n  }\n}\n\nexport function useLocalStorage<T>(key: string, initialValue: T) {\n  const [storedValue, setStoredValue] = useState<T>(() =>\n    readLocalStorage(key, initialValue),\n  )\n  const setValue = (value: T) => {\n    setStoredValue(value)\n    try {\n      globalThis.localStorage.setItem(key, JSON.stringify(value))\n    } catch (error) {\n      console.error(error)\n    }\n  }\n  return [storedValue, setValue] as const\n}\n", "import { timeout } from './fetch'\n\n/**\n * Poll a remote job until it reports done. `check` returns true when finished,\n * false when still pending, and throws on failure. Between checks it counts down\n * `intervalSeconds`, calling `onCountdown` each second so the UI can show\n * progress.\n *\n * `signal` ends the loop with an AbortError: the countdown rejects on the tick\n * it is aborted rather than at the end of the interval, so a cancelled launch\n * stops within a second instead of running for the job's lifetime.\n */\nexport async function pollLoop({\n  check,\n  intervalSeconds,\n  onCountdown,\n  signal,\n}: {\n  check: () => Promise<boolean>\n  intervalSeconds: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n  while (true) {\n    signal?.throwIfAborted()\n    if (await check()) {\n      return\n    }\n    for (let i = intervalSeconds; i > 0; i--) {\n      onCountdown(i)\n      await timeout(1000, signal)\n    }\n  }\n}\n", "import { isAbortError, textfetch } from './fetch'\nimport { pollLoop } from './poll'\nimport { readLocalStorage } from './useLocalStorage'\n\n/**\n * EBI's Job Dispatcher REST services (clustalo, muscle, ncbiblast, ...) all\n * speak the same run/status/result protocol, so the transport lives here and\n * each tool only supplies its own parameters and result types.\n *\n * Unlike NCBI's Blast.cgi these endpoints send `Access-Control-Allow-Origin: *`,\n * which is why the BLAST backend moved here \u2014 see docs/blast.md.\n */\nexport const EBI_BASE = 'https://www.ebi.ac.uk/Tools/services/rest'\n\n/**\n * EBI asks for a contact address on every submission so they can reach whoever\n * is generating the load. The default is the project's mailbox; a deployment\n * that sends real volume should name its own maintainer in the BLAST settings\n * dialog.\n */\nexport const EBI_EMAIL_STORAGE_KEY = 'msa-ebiContactEmail'\nexport const DEFAULT_EBI_EMAIL = 'jbrowse2@berkeley.edu'\n\nexport function getEbiEmail() {\n  const configured = readLocalStorage(\n    EBI_EMAIL_STORAGE_KEY,\n    DEFAULT_EBI_EMAIL,\n  ).trim()\n  return configured || DEFAULT_EBI_EMAIL\n}\n\n/** Statuses that mean the job is over and produced no result. */\nconst FAILED_STATUSES = new Set(['ERROR', 'FAILURE', 'NOT_FOUND'])\n\nasync function submitEbiJob({\n  tool,\n  params,\n  signal,\n}: {\n  tool: string\n  params: Record<string, string>\n  signal?: AbortSignal\n}) {\n  const jobId = await textfetch(`${EBI_BASE}/${tool}/run`, {\n    method: 'POST',\n    body: new URLSearchParams({ email: getEbiEmail(), ...params }),\n    signal,\n  })\n  return jobId.trim()\n}\n\n/**\n * A status check that could not reach EBI at all says nothing about the job, so\n * it is not a reason to abandon one. A job the server has accepted keeps running\n * whatever happens to the poller's connection, and EBI's cluster has answered\n * status checks with a 502 for ten minutes on jobs that then finished (see\n * docs/blast.md).\n *\n * So the poll gives up only once checks have failed without a break for this\n * long: an endpoint that has genuinely gone away must not be polled forever.\n */\nexport const STATUS_FAILURE_BUDGET_MS = 15 * 60 * 1000\n\nexport async function waitForEbiJob({\n  tool,\n  jobId,\n  intervalSeconds = 10,\n  onCountdown,\n  signal,\n}: {\n  tool: string\n  jobId: string\n  intervalSeconds?: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  let failingSince: number | undefined\n  await pollLoop({\n    intervalSeconds,\n    onCountdown,\n    signal,\n    check: async () => {\n      let status: string\n      try {\n        status = (\n          await textfetch(`${EBI_BASE}/${tool}/status/${jobId}`, { signal })\n        ).trim()\n      } catch (e) {\n        // a cancelled request is the caller giving up, not EBI being\n        // unreachable, so it must end the poll rather than be retried\n        if (isAbortError(e)) {\n          throw e\n        }\n        failingSince ??= Date.now()\n        if (Date.now() - failingSince >= STATUS_FAILURE_BUDGET_MS) {\n          throw new Error(\n            `Could not reach EBI to check ${tool} job ${jobId} for ${Math.round(STATUS_FAILURE_BUDGET_MS / 60_000)} minutes`,\n            { cause: e },\n          )\n        }\n        console.warn('[msaview] EBI status check failed, retrying:', e)\n        return false\n      }\n      failingSince = undefined\n      // exact match, not includes(): a job whose status is ERROR must not be\n      // able to poll forever waiting for a FINISHED that will never arrive\n      if (status === 'FINISHED') {\n        return true\n      }\n      if (FAILED_STATUSES.has(status)) {\n        throw new Error(`EBI ${tool} job ${jobId} returned status ${status}`)\n      }\n      // RUNNING, QUEUED, PENDING and anything else EBI adds later\n      return false\n    },\n  })\n}\n\nexport async function runEbiJob({\n  tool,\n  label,\n  params,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  tool: string\n  label: string\n  params: Record<string, string>\n  onProgress: (arg: string) => void\n  onRid?: (jobId: string) => void\n  signal?: AbortSignal\n}) {\n  onProgress(`Submitting ${label} to EBI...`)\n  const jobId = await submitEbiJob({ tool, params, signal })\n  onRid?.(jobId)\n  await waitForEbiJob({\n    tool,\n    jobId,\n    signal,\n    onCountdown: s => {\n      onProgress(`Re-checking ${label} status in... ${s}`)\n    },\n  })\n  return {\n    jobId,\n    result: (type: string) =>\n      textfetch(`${EBI_BASE}/${tool}/result/${jobId}/${type}`, { signal }),\n  }\n}\n", "/**\n * Only used to build the link-out on the manual panel, which sends the user to\n * NCBI's own site to run BLAST there. Nothing fetches this url: NCBI stopped\n * sending Access-Control-Allow-Origin to third-party origins, so a browser\n * cannot read a response from it at all. See docs/blast.md.\n */\nexport const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'\n\n/** The aligners EBI's Job Dispatcher runs, each a tool name at their REST api. */\nexport const ebiMsaAlgorithms = [\n  'clustalo',\n  'muscle',\n  'kalign',\n  'mafft',\n] as const\nexport type EbiMsaAlgorithm = (typeof ebiMsaAlgorithms)[number]\n\n/**\n * `browser` is no job at all: each sequence is aligned to the query in the\n * page and the rows merged on the query (utils/browserAlign.ts), with the tree\n * built by react-msaview's neighbour joining. It is the aligner for a launch\n * that must not depend on EBI, and for one that wants to be quick -- a\n * hundred 400-residue rows take under a second, and a hundred 1400-residue\n * rows eight, against a Job Dispatcher queue that has been measured at\n * anything from ten seconds to fifteen minutes. Past the per-sequence limit in\n * browserAlign.ts it refuses and names an EBI aligner instead.\n */\nexport const msaAlgorithms = [...ebiMsaAlgorithms, 'browser'] as const\nexport type MsaAlgorithm = (typeof msaAlgorithms)[number]\n\nexport const msaAlgorithmLabels: Record<MsaAlgorithm, string> = {\n  clustalo: 'Clustal Omega (EBI)',\n  muscle: 'MUSCLE (EBI)',\n  kalign: 'Kalign (EBI)',\n  mafft: 'MAFFT (EBI)',\n  browser: 'in browser, query-anchored',\n}\n\n/**\n * EBI rejects a submission naming a database outside its own list with a 400,\n * so every value here has to appear in\n * https://www.ebi.ac.uk/Tools/services/rest/ncbiblast/parameterdetails/database\n * -- `uniprotkb_reference_proteomes` did not, and 3.0.0 shipped it as a dead\n * menu entry.\n */\nexport const blastDatabaseOptions = [\n  'uniprotkb_swissprot',\n  'uniprotkb',\n  'pan_proteomes',\n  'uniprotkb_trembl',\n] as const\nexport type BlastDatabase = (typeof blastDatabaseOptions)[number]\n\n// curated, so it returns roughly one good sequence per species rather than the\n// many near-identical TrEMBL entries an alignment reads poorly\nconst defaultBlastDatabase: BlastDatabase = 'uniprotkb_swissprot'\n\nexport const searchPrograms = ['blastp', 'phmmer'] as const\nexport type SearchProgram = (typeof searchPrograms)[number]\n\nexport const searchProgramLabels: Record<SearchProgram, string> = {\n  blastp: 'blastp (sequence search)',\n  phmmer: 'phmmer (profile HMM search)',\n}\n\n/**\n * phmmer offers PDB, AlphaFold, Ensembl Genomes, MEROPS and ChEMBL too, but\n * targets outside UniProt carry no species in their description, so those rows\n * would lose their species and common name. Only the databases that label their\n * hits are offered.\n *\n * rp15..rp75 are the Representative Proteomes: UniProt's reference proteomes\n * thinned so that no two are more than 15% (35%, 55%, 75%) similar, which is\n * the widest taxonomic spread per hit that any of these databases gives. rp15\n * is the one to reach for when the question is \"what is this like across all\n * of life\"; swissprot when it is \"what is this like in the curated set\".\n */\nexport const phmmerDatabaseOptions = [\n  'swissprot',\n  'uniprotkb',\n  'uniprotrefprot',\n  'rp75',\n  'rp55',\n  'rp35',\n  'rp15',\n] as const\nexport type PhmmerDatabase = (typeof phmmerDatabaseOptions)[number]\n\nconst defaultPhmmerDatabase: PhmmerDatabase = 'swissprot'\n\n/**\n * The hit counts EBI's ncbiblast accepts for `alignments` and `scores`. A value\n * off this list is a 400 at submit time, so a request is rounded up to the next\n * one on it.\n */\nconst blastHitCounts = [5, 10, 20, 50, 100, 150, 200, 250, 500, 750, 1000]\n\nexport const defaultMaxHits = 100\n\nexport function snapBlastHitCount(maxHits: number) {\n  return blastHitCounts.find(n => n >= maxHits) ?? blastHitCounts.at(-1)!\n}\n\n/**\n * A program together with a database that program actually has.\n *\n * The pair travels as one value because neither service knows the other's\n * database names \u2014 `swissprot` is a phmmer database and `uniprotkb_swissprot` a\n * blastp one \u2014 so a program held apart from its database can drift into a\n * combination EBI answers with a 400, minutes after the user pressed Submit.\n */\nexport type SearchChoice =\n  | { program: 'blastp'; database: BlastDatabase }\n  | { program: 'phmmer'; database: PhmmerDatabase }\n\nexport function defaultSearchFor(program: SearchProgram): SearchChoice {\n  return program === 'phmmer'\n    ? { program, database: defaultPhmmerDatabase }\n    : { program, database: defaultBlastDatabase }\n}\n\nexport function databaseOptionsFor(program: SearchProgram) {\n  return program === 'phmmer' ? phmmerDatabaseOptions : blastDatabaseOptions\n}\n\n/**\n * What each database is called in the menu. The keys are what EBI is sent and\n * are not negotiable; `uniprotkb_swissprot` and `swissprot` are the same\n * collection under each service's own name, so they read the same here.\n */\nconst databaseLabels: Record<BlastDatabase | PhmmerDatabase, string> = {\n  uniprotkb_swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  uniprotkb: 'UniProtKB (all entries)',\n  uniprotkb_trembl: 'UniProtKB/TrEMBL (unreviewed)',\n  pan_proteomes: 'Pan-proteomes',\n  uniprotrefprot: 'UniProt reference proteomes',\n  rp75: 'Representative proteomes, 75%',\n  rp55: 'Representative proteomes, 55%',\n  rp35: 'Representative proteomes, 35%',\n  rp15: 'Representative proteomes, 15% (widest spread)',\n}\n\nexport function databaseLabel(database: BlastDatabase | PhmmerDatabase) {\n  return databaseLabels[database]\n}\n", "import type { Node, NodeWithIds } from './types.ts'\n\n/**\n * Copy a parsed tree, giving every node a stable id derived from its path, and\n * falling back to that id for an unnamed node.\n *\n * Iterative, like the traversals in @gmod/newick and the Newick emitter in the\n * viewer's neighbor joining: a phylogeny can be a caterpillar whose depth equals\n * its leaf count, and the recursive form of this overflowed the stack somewhere\n * past 5000 deep -- which every tree reaches, since this is the last step of\n * parsing one.\n */\nexport function generateNodeIds(\n  tree: Node,\n  parent = 'node',\n  depth = 0,\n): NodeWithIds {\n  const withId = (node: Node, id: string): NodeWithIds => ({\n    ...node,\n    id,\n    name: node.name || id,\n    children: [],\n  })\n\n  const root = withId(tree, `${parent}-${depth}`)\n  const stack = [{ src: tree, out: root, depth }]\n  while (stack.length > 0) {\n    const { src, out, depth: d } = stack.pop()!\n    if (src.children) {\n      out.children = src.children.map((child, i) =>\n        withId(child, `${out.id}-${i}-${d + 1}`),\n      )\n      for (const [i, child] of src.children.entries()) {\n        stack.push({ src: child, out: out.children[i]!, depth: d + 1 })\n      }\n    }\n  }\n  return root\n}\n", "import type { MSATrack, NodeWithIds } from '../types.ts'\n\nexport default abstract class BaseMSA {\n  protected rows = new Map<string, string>()\n  private names: string[]\n  private width?: number\n\n  /**\n   * A repeated name keeps its first row: names index the rows, so listing the\n   * name twice would render a phantom duplicate row.\n   */\n  constructor(rows: Iterable<readonly [string, string]>) {\n    for (const [name, seq] of rows) {\n      if (!this.rows.has(name)) {\n        this.rows.set(name, seq)\n      }\n    }\n    this.names = [...this.rows.keys()]\n  }\n\n  getRow(name: string): string {\n    return this.rows.get(name) ?? ''\n  }\n\n  getNames(): string[] {\n    return this.names\n  }\n\n  /**\n   * Column count of the alignment: the length of its widest row, since a\n   * hand-edited fasta or some aligners leave rows short. The viewer's gap\n   * analysis counts columns the same way.\n   */\n  getWidth(): number {\n    this.width ??= this.getNames().reduce(\n      (max, name) => Math.max(max, this.getRow(name).length),\n      0,\n    )\n    return this.width\n  }\n\n  getTree(): NodeWithIds {\n    return {\n      id: 'root',\n      name: 'root',\n      noTree: true,\n      children: this.getNames().map(name => ({\n        id: name,\n        children: [],\n        name,\n      })),\n    }\n  }\n\n  getRowData(\n    _name: string,\n  ): { name?: string; accession?: string; dbxref?: string } | undefined {\n    return undefined\n  }\n\n  getStructures(): Record<string, unknown> {\n    return {}\n  }\n\n  getHeader(): Record<string, unknown> {\n    return {}\n  }\n\n  get alignmentNames(): string[] {\n    return []\n  }\n\n  get seqConsensus(): string | undefined {\n    return undefined\n  }\n\n  get secondaryStructureConsensus(): string | undefined {\n    return undefined\n  }\n\n  get tracks(): MSATrack[] {\n    return []\n  }\n}\n", "import { parseNewick } from '@gmod/newick'\n\nimport type { NewickNode } from '@gmod/newick'\n\n/**\n * Newick parsing for phylogenetic trees.\n *\n * `postParenNumeric: 'name'` is the whole reason this wrapper exists. A bare\n * number after a `)` is an internal node label in standard Newick -- typically a\n * bootstrap support value -- but `@gmod/hclust` reuses that slot for a cluster's\n * merge height, and the parser's default guesses between the two by whether the\n * tree carries any `:` branch length. Everything reaching this package is a\n * phylogeny (newick, the tree embedded in Stockholm `#=GF NH`, EMF, ASN.1), so\n * the guess is settled here instead: reading `((A,B)95,(C,D)80);` as lengths\n * would draw a phylogram scaled by support values.\n */\nexport default function parse(s: string): NewickNode {\n  return parseNewick(s, { postParenNumeric: 'name' })\n}\n", "/**\n * Stockholm format parser\n * Based on stockholm-js by Ian Holmes\n * Rewritten in TypeScript\n */\n\nexport interface StockholmData {\n  gf: Record<string, string[]>\n  gc: Record<string, string>\n  gs: Record<string, Record<string, string[]>>\n  gr: Record<string, Record<string, string>>\n  seqname: string[]\n  seqdata: Record<string, string>\n}\n\nfunction createStockholm(): StockholmData {\n  return {\n    gf: Object.create(null),\n    gc: Object.create(null),\n    gs: Object.create(null),\n    gr: Object.create(null),\n    seqname: [],\n    seqdata: Object.create(null),\n  }\n}\n\n// records before a \"# STOCKHOLM 1.0\" header are an error in strict mode,\n// otherwise they implicitly start a new alignment\nfunction ensureStock(\n  stock: StockholmData | null,\n  strict: boolean,\n): StockholmData {\n  if (stock) {\n    return stock\n  }\n  if (strict) {\n    throw new Error('No format header: # STOCKHOLM 1.0')\n  }\n  return createStockholm()\n}\n\nconst formatStartRegex = /^# STOCKHOLM 1.0/\nconst formatEndRegex = /^\\/\\/\\s*$/\nconst gfRegex = /^#=GF\\s+(\\S+)\\s+(.*?)\\s*$/\nconst gcRegex = /^#=GC\\s+(\\S+)\\s+(.*?)\\s*$/\nconst gsRegex = /^#=GS\\s+(\\S+)\\s+(\\S+)\\s+(.*?)\\s*$/\nconst grRegex = /^#=GR\\s+(\\S+)\\s+(\\S+)\\s+(.*?)\\s*$/\n// a sequence line is \"<name> <residues>\". The leading [^#\\s] guards against a\n// two-word comment (\"# note\") being taken as a sequence named '#'; every\n// meaningful '#' line is a #=GF/#=GC/#=GS/#=GR record already matched above.\nconst lineRegex = /^\\s*([^#\\s]\\S*)\\s+(\\S+)\\s*$/\nconst nonwhiteRegex = /\\S/\n\nexport function sniff(text: string): boolean {\n  return formatStartRegex.test(text)\n}\n\nexport function parseAll(\n  text: string,\n  opts?: { strict?: boolean },\n): StockholmData[] {\n  const options = opts ?? {}\n  const db: StockholmData[] = []\n  let stock: StockholmData | null = null\n  // one tree spans consecutive `#=GF NH` lines, so a `#=GF TN` naming the\n  // next tree, or any other #=GF line, ends it\n  let treeContinues = false\n\n  const lines = text.split('\\n')\n  for (const line of lines) {\n    let match: RegExpExecArray | null\n\n    if (formatStartRegex.test(line)) {\n      if (stock) {\n        db.push(stock)\n      }\n      stock = createStockholm()\n      treeContinues = false\n    } else if (formatEndRegex.test(line)) {\n      if (stock) {\n        db.push(stock)\n      }\n      stock = null\n    } else if ((match = gfRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const tag = match[1]!\n      const values = (stock.gf[tag] ??= [])\n      if (tag === 'NH' && treeContinues && values.length > 0) {\n        values[values.length - 1] += match[2]!\n      } else {\n        values.push(match[2]!)\n      }\n      treeContinues = tag === 'NH'\n    } else if ((match = gcRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      stock.gc[match[1]!] = (stock.gc[match[1]!] ?? '') + match[2]!\n    } else if ((match = gsRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const byName = (stock.gs[match[2]!] ??= Object.create(null))\n      ;(byName[match[1]!] ??= []).push(match[3]!)\n    } else if ((match = grRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const byName = (stock.gr[match[2]!] ??= Object.create(null))\n      byName[match[1]!] = (byName[match[1]!] ?? '') + match[3]!\n    } else if ((match = lineRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const seqname = match[1]!\n      const seqdata = match[2]!\n      if (stock.seqdata[seqname] === undefined) {\n        stock.seqdata[seqname] = ''\n        stock.seqname.push(seqname)\n      }\n      stock.seqdata[seqname] += seqdata\n    } else if (nonwhiteRegex.test(line)) {\n      if (options.strict) {\n        throw new Error('Malformed line')\n      }\n    }\n  }\n\n  if (stock) {\n    db.push(stock)\n  }\n\n  return db\n}\n\nexport function parse(\n  text: string,\n  opts?: { strict?: boolean },\n): StockholmData {\n  const db = parseAll(text, opts)\n  if (db.length === 0) {\n    throw new Error('No alignments found')\n  }\n  if (db.length > 1) {\n    throw new Error('More than one alignment found')\n  }\n  return db[0]!\n}\n", "import { generateNodeIds } from '../util.ts'\nimport BaseMSA from './BaseMSA.ts'\nimport parseNewick from './parseNewick.ts'\nimport { parseAll } from './stockholmParser.ts'\n\nimport type { MSATrack, NodeWithIds } from '../types.ts'\nimport type { StockholmData } from './stockholmParser.ts'\n\nexport default class StockholmMSA extends BaseMSA {\n  private data: StockholmData[]\n  private MSA: StockholmData\n\n  constructor(text: string, currentAlignment: number) {\n    const res = parseAll(text)\n    const aln = res[currentAlignment] ?? res[0]\n    if (!aln) {\n      throw new Error('No alignments found in Stockholm file')\n    }\n    super(aln.seqname.map(name => [name, aln.seqdata[name] ?? '']))\n    this.data = res\n    this.MSA = aln\n  }\n\n  getMSA() {\n    return this.MSA\n  }\n\n  get alignmentNames() {\n    return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`)\n  }\n\n  getHeader() {\n    const acEntries = this.MSA.gs.AC ?? {}\n    const drEntries = this.MSA.gs.DR ?? {}\n    return {\n      General: this.MSA.gf,\n      Accessions: Object.fromEntries(\n        Object.entries(acEntries).map(([k, v]) => [k, v[0]]),\n      ),\n      Dbxref: Object.fromEntries(\n        Object.entries(drEntries).map(([k, v]) => [k, v.join('; ')]),\n      ),\n    }\n  }\n\n  getRowData(rowName: string) {\n    return {\n      name: rowName,\n      accession: this.MSA.gs.AC?.[rowName]?.[0],\n      dbxref: this.MSA.gs.DR?.[rowName]?.join('; '),\n    }\n  }\n\n  getStructures() {\n    const pdbRegex = /PDB; +(\\S+) +([^;\\s]+); *(-?[0-9]+)-(-?[0-9]+)/\n    const drEntries = this.MSA.gs.DR ?? {}\n    const result: Record<\n      string,\n      { pdb: string; chain: string; startPos: number; endPos: number }[]\n    > = {}\n    for (const [id, drList] of Object.entries(drEntries)) {\n      for (const dr of drList) {\n        const match = pdbRegex.exec(dr)\n        if (match) {\n          ;(result[id] ??= []).push({\n            pdb: match[1]!.toLowerCase(),\n            chain: match[2]!,\n            startPos: +match[3]!,\n            endPos: +match[4]!,\n          })\n        }\n      }\n    }\n    return result\n  }\n\n  getTree(): NodeWithIds {\n    const tree = this.MSA.gf.NH?.[0]\n    return tree ? generateNodeIds(parseNewick(tree)) : super.getTree()\n  }\n\n  get seqConsensus() {\n    return this.MSA.gc.seq_cons\n  }\n\n  get secondaryStructureConsensus() {\n    return this.MSA.gc.SS_cons\n  }\n\n  /**\n   * One text track per `#=GC` line, and one per `#=GR` line that stays hidden\n   * until asked for: a Pfam seed carries a few per-row active-site lines, but\n   * an Rfam family carries a structure line for every row with a PDB entry.\n   */\n  get tracks(): MSATrack[] {\n    const { seq_cons, SS_cons, ...otherGc } = this.MSA.gc\n    return [\n      {\n        id: 'seqConsensus',\n        name: 'Sequence consensus',\n        data: seq_cons,\n        customColorScheme: {},\n      },\n      {\n        id: 'secondaryStruct',\n        name: 'Secondary-structure',\n        data: SS_cons,\n        customColorScheme: wussColors,\n      },\n      ...Object.entries(otherGc).map(([tag, data]) => ({\n        id: `gc-${tag}`,\n        name: tag,\n        data,\n        customColorScheme: structureColors(tag),\n      })),\n      ...Object.entries(this.MSA.gr).flatMap(([tag, byRow]) =>\n        Object.entries(byRow).map(([row, data]) => ({\n          id: `gr-${row}-${tag}`,\n          name: `${row} ${tag}`,\n          data,\n          customColorScheme: structureColors(tag),\n          defaultOff: true,\n        })),\n      ),\n    ]\n  }\n}\n\n// WUSS writes base-paired columns as open/close brackets of several nesting\n// types (<>, (), [], {}); coloring every open one way and every close the other\n// highlights each helix, including the tRNA acceptor stem written with parens\nconst wussColors: Record<string, string> = {\n  '<': 'lightblue',\n  '(': 'lightblue',\n  '[': 'lightblue',\n  '{': 'lightblue',\n  '>': 'pink',\n  ')': 'pink',\n  ']': 'pink',\n  '}': 'pink',\n}\n\n// `SS`, and Rfam's per-structure `2GIS_A_SS`\nfunction structureColors(tag: string) {\n  return tag === 'SS' || tag.endsWith('_SS') ? wussColors : {}\n}\n\nexport { sniff as stockholmSniff } from './stockholmParser.ts'\n", "export interface FastaRecord {\n  id: string\n  seq: string\n}\n\n// a `>` record, optionally after `#` header lines such as ColabFold's `#8\\t1`\nexport function fastaSniff(text: string) {\n  return /^(#.*\\n)*>/.test(text)\n}\n\n/**\n * Split FASTA-style text (shared by the FASTA and A3M parsers) into records.\n *\n * A record starts at a `>` that begins a line, so a `>` inside a defline\n * (`x->y`, HGVS `c.1799T>A`) stays part of it, and anything before the first\n * record (ColabFold's `#8\\t1` header) is skipped. The id is the first word of\n * the defline, so `> name` reads as `name`, and a defline with no word names\n * its record `unnamed_N` after its position in the file. A repeated id keeps\n * the first record: ids index the row data, so emitting the id twice would\n * render a phantom duplicate row showing the last record's residues.\n */\nexport function splitFastaRecords(text: string): FastaRecord[] {\n  const records: FastaRecord[] = []\n  const seen = new Set<string>()\n  let current: { id: string; lines: string[] } | undefined\n\n  const flush = () => {\n    if (current && !seen.has(current.id)) {\n      seen.add(current.id)\n      records.push({\n        id: current.id,\n        seq: current.lines.join('').replaceAll(/\\s/g, ''),\n      })\n    }\n  }\n\n  let count = 0\n  for (const line of text.split('\\n')) {\n    if (line.startsWith('>')) {\n      flush()\n      count++\n      const id = /^>\\s*(\\S*)/.exec(line)![1] || `unnamed_${count}`\n      current = { id, lines: [] }\n    } else {\n      current?.lines.push(line)\n    }\n  }\n  flush()\n\n  return records\n}\n\nexport function toRecords(input: string | FastaRecord[]) {\n  return typeof input === 'string' ? splitFastaRecords(input) : input\n}\n", "import BaseMSA from './BaseMSA.ts'\nimport { fastaSniff, toRecords } from './fastaRecords.ts'\n\nimport type { FastaRecord } from './fastaRecords.ts'\n\n/**\n * A3M Format Parser\n *\n * The A3M format consists of aligned FASTA, in which alignments are shown with:\n * - Inserts as lowercase characters\n * - Matches as uppercase characters\n * - Deletions as '-'\n * - Gaps aligned to inserts as '.'\n *\n * Note that gaps aligned to inserts can be omitted in the A3M format.\n *\n * Example:\n * >query\n * ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE\n * >seq1\n * ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP-----------\n *\n * In the above, 'e' after 'G' in seq1 is a lowercase insert.\n *\n * @see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html\n */\n\nconst CODE_A = 65 // 'A'\nconst CODE_Z = 90 // 'Z'\nconst CODE_a = 97 // 'a'\nconst CODE_z = 122 // 'z'\nconst CODE_DASH = 45 // '-'\n\nfunction isLower(code: number): boolean {\n  return code >= CODE_a && code <= CODE_z\n}\n\nfunction isMatch(code: number): boolean {\n  return (code >= CODE_A && code <= CODE_Z) || code === CODE_DASH\n}\n\ninterface ParsedRow {\n  // one entry per match column, in order\n  matches: string[]\n  // inserts[k] is the run of insert residues sitting immediately BEFORE match\n  // column k, already uppercased; inserts[matches.length] holds the trailing\n  // run. An insert must never consume a match column, or a row that opens with\n  // an insert falls a column out of register with every other row.\n  inserts: string[]\n}\n\nfunction parseRow(seq: string): ParsedRow {\n  const matches: string[] = []\n  const inserts = ['']\n\n  for (const ch of seq) {\n    const code = ch.charCodeAt(0)\n    if (isMatch(code)) {\n      matches.push(ch)\n      inserts.push('')\n    } else if (isLower(code)) {\n      inserts[inserts.length - 1] += ch.toUpperCase()\n    }\n    // '.' is padding aligned to some other row's insert, and anything else is\n    // unrecognized -- neither carries alignment information\n  }\n\n  return { matches, inserts }\n}\n\nexport default class A3mMSA extends BaseMSA {\n  constructor(input: string | FastaRecord[]) {\n    const records = toRecords(input)\n    const expanded = expandA3M(records.map(r => r.seq))\n    super(records.map((r, i) => [r.id, expanded[i]!]))\n  }\n\n  static sniff(input: string | FastaRecord[]): boolean {\n    if (typeof input === 'string' && !fastaSniff(input)) {\n      return false\n    }\n\n    const seqs = toRecords(input)\n      .map(r => r.seq)\n      .filter(s => !!s)\n\n    if (seqs.length < 2) {\n      return false\n    }\n\n    // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked\n    // references) has all rows the same total length. A3M's defining feature is\n    // variable-length rows, since lowercase inserts live outside the fixed match\n    // grid. So equal-length rows are an alignment, not A3M, even when lowercase\n    // soft-masking is present.\n    if (new Set(seqs.map(s => s.length)).size === 1) {\n      return false\n    }\n\n    let hasLowercase = false\n    let matchCount: number | undefined\n    for (const seq of seqs) {\n      let matches = 0\n      for (let i = 0; i < seq.length; i++) {\n        const code = seq.charCodeAt(i)\n        if (isMatch(code)) {\n          matches++\n        } else if (isLower(code)) {\n          hasLowercase = true\n        }\n      }\n      if (matchCount !== undefined && matches !== matchCount) {\n        return false\n      }\n      matchCount = matches\n    }\n    return hasLowercase\n  }\n}\n\n/**\n * Expand A3M rows into a rectangular alignment: every insert slot is widened to\n * the longest insert any row places there, and rows without one are padded with\n * '.' so all rows stay in register.\n */\nfunction expandA3M(rawSeqs: string[]): string[] {\n  const rows = rawSeqs.map(parseRow)\n  // a loop, not Math.max(...): an a3m from an hhblits search routinely carries\n  // six figures of hits, and spreading one argument per row throws\n  // \"Maximum call stack size exceeded\" somewhere past ~125k of them\n  let numPositions = 0\n  for (const { matches } of rows) {\n    numPositions = Math.max(numPositions, matches.length)\n  }\n\n  // one insert slot before each match column, plus one trailing slot\n  const maxInserts = new Array<number>(numPositions + 1).fill(0)\n  for (const { inserts } of rows) {\n    for (const [pos, ins] of inserts.entries()) {\n      maxInserts[pos] = Math.max(maxInserts[pos]!, ins.length)\n    }\n  }\n\n  return rows.map(({ matches, inserts }) => {\n    const result: string[] = []\n    for (let pos = 0; pos <= numPositions; pos++) {\n      const ins = inserts[pos] ?? ''\n      result.push(ins, '.'.repeat(maxInserts[pos]! - ins.length))\n      if (pos < numPositions) {\n        // a row with fewer match columns than the widest is padded out\n        result.push(matches[pos] ?? '-')\n      }\n    }\n    return result.join('')\n  })\n}\n", "import { parse } from 'clustal-js'\n\nimport BaseMSA from './BaseMSA.ts'\n\nexport default class ClustalMSA extends BaseMSA {\n  private MSA: ReturnType<typeof parse>\n\n  constructor(text: string) {\n    const msa = parse(text)\n    super(msa.alns.map(aln => [aln.id, aln.seq]))\n    this.MSA = msa\n  }\n\n  getHeader() {\n    return this.MSA.header\n  }\n\n  get seqConsensus() {\n    return this.MSA.consensus\n  }\n}\n", "import { parseEmfAln } from 'emf-js'\n\nimport BaseMSA from './BaseMSA.ts'\n\nexport default class EmfMSA extends BaseMSA {\n  constructor(text: string) {\n    super(parseEmfAln(text).map(aln => [aln.protein, aln.seq]))\n  }\n}\n", "import BaseMSA from './BaseMSA.ts'\nimport { toRecords } from './fastaRecords.ts'\n\nimport type { FastaRecord } from './fastaRecords.ts'\n\nexport default class FastaMSA extends BaseMSA {\n  // Newick tools write a colon in a name as an underscore\n  private colonNormalized = new Map<string, string>()\n\n  constructor(input: string | FastaRecord[]) {\n    const records = toRecords(input)\n    super(records.map(r => [r.id, r.seq]))\n    for (const { id } of records) {\n      if (id.includes(':')) {\n        this.colonNormalized.set(id.replaceAll(':', '_'), id)\n      }\n    }\n  }\n\n  getRow(name: string) {\n    return (\n      this.rows.get(name) ??\n      this.rows.get(this.colonNormalized.get(name) ?? '') ??\n      ''\n    )\n  }\n}\n", "import A3mMSA from './A3mMSA.ts'\nimport ClustalMSA from './ClustalMSA.ts'\nimport EmfMSA from './EmfMSA.ts'\nimport FastaMSA from './FastaMSA.ts'\nimport StockholmMSA, { stockholmSniff } from './StockholmMSA.ts'\nimport { fastaSniff, splitFastaRecords } from './fastaRecords.ts'\n\nexport { parseEmfTree } from 'emf-js'\nexport { default as parseNewick } from './parseNewick.ts'\n\nexport type MSAParserType =\n  | StockholmMSA\n  | A3mMSA\n  | FastaMSA\n  | EmfMSA\n  | ClustalMSA\n\nexport type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'\n\nconst htmlPage = /^<(!doctype\\s+html|html[\\s>])/i\nconst clustalHeader = /^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i\n\n// A caller that knows the format, such as impg emitting fasta-aln, passes\n// `format` to skip sniffing, which cannot always tell FASTA from A3M\nexport function parseMSA(\n  input: string,\n  currentAlignment = 0,\n  format?: MSAFormat,\n): MSAParserType {\n  const text = input\n    .replace(/^\\uFEFF/, '')\n    .replaceAll(/\\r\\n?/g, '\\n')\n    .trimStart()\n  if (htmlPage.test(text)) {\n    throw new Error(\n      'Received an HTML page, not an alignment. Check that the URL points at the file itself',\n    )\n  }\n  if (format === 'stockholm') {\n    return new StockholmMSA(text, currentAlignment)\n  }\n  if (format === 'a3m') {\n    return new A3mMSA(text)\n  }\n  if (format === 'fasta') {\n    return new FastaMSA(text)\n  }\n  if (format === 'emf') {\n    return new EmfMSA(text)\n  }\n  if (format === 'clustal') {\n    return new ClustalMSA(text)\n  }\n  if (stockholmSniff(text)) {\n    return new StockholmMSA(text, currentAlignment)\n  }\n  if (fastaSniff(text)) {\n    const records = splitFastaRecords(text)\n    return A3mMSA.sniff(records) ? new A3mMSA(records) : new FastaMSA(records)\n  }\n  if (text.startsWith('SEQ')) {\n    return new EmfMSA(text)\n  }\n  if (clustalHeader.test(text)) {\n    return new ClustalMSA(text)\n  }\n  const firstLine = text.split('\\n', 1)[0]!.slice(0, 80)\n  throw new Error(\n    firstLine\n      ? `Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads \"${firstLine}\"`\n      : 'The alignment file is empty',\n  )\n}\n\n/**\n * Get ungapped sequence from an aligned row\n */\nexport function getUngappedSequence(alignedSeq: string): string {\n  return alignedSeq.replaceAll(/[.-]/g, '')\n}\n\nexport { default as A3mMSA } from './A3mMSA.ts'\nexport { default as ClustalMSA } from './ClustalMSA.ts'\nexport { default as EmfMSA } from './EmfMSA.ts'\nexport { default as FastaMSA } from './FastaMSA.ts'\nexport { default as StockholmMSA, stockholmSniff } from './StockholmMSA.ts'\n"],
+  "mappings": "uKAAA,SAASA,EAAOC,EAAa,CAC3B,GAAI,CACF,OAAO,IAAI,IAAIA,CAAG,EAAE,IACtB,MAAQ,CAEN,OAAOA,CACT,CACF,CAEO,IAAMC,EAAN,cAAwB,KAAM,CACnC,YACEC,EACSC,EACT,CACA,MAAMD,CAAO,EAFJ,YAAAC,CAGX,CACF,EAEA,eAAsBC,EAAYJ,EAAaK,EAAoB,CACjE,IAAIC,EACJ,GAAI,CACFA,EAAW,MAAM,MAAMN,EAAKK,CAAI,CAClC,OAASE,EAAG,CAMV,MAAIA,aAAa,UACT,IAAI,MACR,mBAAmBR,EAAOC,CAAG,CAAC,4LAC9B,CAAE,MAAOO,CAAE,CACb,EAEIA,CACR,CAEA,GAAI,CAACD,EAAS,GACZ,MAAM,IAAIL,EACR,QAAQK,EAAS,MAAM,aAAaN,CAAG,KAAK,MAAMM,EAAS,KAAK,GAAG,MAAM,EAAG,GAAG,CAAC,GAChFA,EAAS,MACX,EAGF,OAAOA,CACT,CAEA,eAAsBE,EAAUR,EAAaK,EAAoB,CAE/D,OADiB,MAAMD,EAAYJ,EAAKK,CAAI,GAC5B,KAAK,CACvB,CAEA,eAAsBI,GAAaT,EAAaK,EAAoB,CAElE,OADiB,MAAMD,EAAYJ,EAAKK,CAAI,GAC5B,KAAK,CACvB,CAEO,SAASK,EAAQC,EAAcC,EAAsB,CAC1D,OAAO,IAAI,QAAc,CAACC,EAASC,IAAW,CAC5C,GAAIF,GAAQ,QAAS,CACnBE,EAAO,IAAI,aAAa,UAAW,YAAY,CAAC,EAChD,MACF,CAIA,IAAMC,EAAU,IAAM,CACpB,aAAaC,CAAE,EACfF,EAAO,IAAI,aAAa,UAAW,YAAY,CAAC,CAClD,EACME,EAAK,WAAW,IAAM,CAC1BJ,GAAQ,oBAAoB,QAASG,CAAO,EAC5CF,EAAQ,CACV,EAAGF,CAAI,EACPC,GAAQ,iBAAiB,QAASG,EAAS,CAAE,KAAM,EAAK,CAAC,CAC3D,CAAC,CACH,CAQO,SAASE,EAAa,EAAY,CACvC,OAAO,aAAa,OAAS,EAAE,OAAS,YAC1C,CCtFA,IAAAC,EAAyB,OAOlB,SAASC,EAAoBC,EAAaC,EAAoB,CACnE,GAAI,CACF,IAAMC,EAAO,WAAW,aAAa,QAAQF,CAAG,EAChD,OAAOE,IAAS,KAAOD,EAAgB,KAAK,MAAMC,CAAI,CACxD,OAASC,EAAO,CACd,eAAQ,MAAMA,CAAK,EACZF,CACT,CACF,CAEO,SAASG,GAAmBJ,EAAaC,EAAiB,CAC/D,GAAM,CAACI,EAAaC,CAAc,KAAI,YAAY,IAChDP,EAAiBC,EAAKC,CAAY,CACpC,EASA,MAAO,CAACI,EARUE,GAAa,CAC7BD,EAAeC,CAAK,EACpB,GAAI,CACF,WAAW,aAAa,QAAQP,EAAK,KAAK,UAAUO,CAAK,CAAC,CAC5D,OAASJ,EAAO,CACd,QAAQ,MAAMA,CAAK,CACrB,CACF,CAC6B,CAC/B,CClBA,eAAsBK,EAAS,CAC7B,MAAAC,EACA,gBAAAC,EACA,YAAAC,EACA,OAAAC,CACF,EAKG,CAED,OAAa,CAEX,GADAA,GAAQ,eAAe,EACnB,MAAMH,EAAM,EACd,OAEF,QAASI,EAAIH,EAAiBG,EAAI,EAAGA,IACnCF,EAAYE,CAAC,EACb,MAAMC,EAAQ,IAAMF,CAAM,CAE9B,CACF,CCtBO,IAAMG,EAAW,4CAQXC,EAAwB,sBACxBC,EAAoB,wBAE1B,SAASC,GAAc,CAK5B,OAJmBC,EACjBH,EACAC,CACF,EAAE,KAAK,GACcA,CACvB,CAGA,IAAMG,EAAkB,IAAI,IAAI,CAAC,QAAS,UAAW,WAAW,CAAC,EAEjE,eAAeC,EAAa,CAC1B,KAAAC,EACA,OAAAC,EACA,OAAAC,CACF,EAIG,CAMD,OALc,MAAMC,EAAU,GAAGV,CAAQ,IAAIO,CAAI,OAAQ,CACvD,OAAQ,OACR,KAAM,IAAI,gBAAgB,CAAE,MAAOJ,EAAY,EAAG,GAAGK,CAAO,CAAC,EAC7D,OAAAC,CACF,CAAC,GACY,KAAK,CACpB,CAYO,IAAME,EAA2B,IAAU,IAElD,eAAsBC,GAAc,CAClC,KAAAL,EACA,MAAAM,EACA,gBAAAC,EAAkB,GAClB,YAAAC,EACA,OAAAN,CACF,EAMG,CACD,IAAIO,EACJ,MAAMC,EAAS,CACb,gBAAAH,EACA,YAAAC,EACA,OAAAN,EACA,MAAO,SAAY,CACjB,IAAIS,EACJ,GAAI,CACFA,GACE,MAAMR,EAAU,GAAGV,CAAQ,IAAIO,CAAI,WAAWM,CAAK,GAAI,CAAE,OAAAJ,CAAO,CAAC,GACjE,KAAK,CACT,OAASU,EAAG,CAGV,GAAIC,EAAaD,CAAC,EAChB,MAAMA,EAGR,GADAH,IAAiB,KAAK,IAAI,EACtB,KAAK,IAAI,EAAIA,GAAgBL,EAC/B,MAAM,IAAI,MACR,gCAAgCJ,CAAI,QAAQM,CAAK,QAAQ,KAAK,MAAMF,EAA2B,GAAM,CAAC,WACtG,CAAE,MAAOQ,CAAE,CACb,EAEF,eAAQ,KAAK,+CAAgDA,CAAC,EACvD,EACT,CAIA,GAHAH,EAAe,OAGXE,IAAW,WACb,MAAO,GAET,GAAIb,EAAgB,IAAIa,CAAM,EAC5B,MAAM,IAAI,MAAM,OAAOX,CAAI,QAAQM,CAAK,oBAAoBK,CAAM,EAAE,EAGtE,MAAO,EACT,CACF,CAAC,CACH,CAEA,eAAsBG,GAAU,CAC9B,KAAAd,EACA,MAAAe,EACA,OAAAd,EACA,WAAAe,EACA,MAAAC,EACA,OAAAf,CACF,EAOG,CACDc,EAAW,cAAcD,CAAK,YAAY,EAC1C,IAAMT,EAAQ,MAAMP,EAAa,CAAE,KAAAC,EAAM,OAAAC,EAAQ,OAAAC,CAAO,CAAC,EACzD,OAAAe,IAAQX,CAAK,EACb,MAAMD,GAAc,CAClB,KAAAL,EACA,MAAAM,EACA,OAAAJ,EACA,YAAagB,GAAK,CAChBF,EAAW,eAAeD,CAAK,iBAAiBG,CAAC,EAAE,CACrD,CACF,CAAC,EACM,CACL,MAAAZ,EACA,OAASa,GACPhB,EAAU,GAAGV,CAAQ,IAAIO,CAAI,WAAWM,CAAK,IAAIa,CAAI,GAAI,CAAE,OAAAjB,CAAO,CAAC,CACvE,CACF,CC/IO,IAAMkB,GAAiB,2CAGjBC,GAAmB,CAC9B,WACA,SACA,SACA,OACF,EAaaC,GAAgB,CAAC,GAAGD,GAAkB,SAAS,EAG/CE,GAAmD,CAC9D,SAAU,sBACV,OAAQ,eACR,OAAQ,eACR,MAAO,cACP,QAAS,4BACX,EASaC,GAAuB,CAClC,sBACA,YACA,gBACA,kBACF,EAKMC,GAAsC,sBAE/BC,GAAiB,CAAC,SAAU,QAAQ,EAGpCC,GAAqD,CAChE,OAAQ,2BACR,OAAQ,6BACV,EAcaC,GAAwB,CACnC,YACA,YACA,iBACA,OACA,OACA,OACA,MACF,EAGMC,GAAwC,YAOxCC,EAAiB,CAAC,EAAG,GAAI,GAAI,GAAI,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,GAAI,EAE5DC,GAAiB,IAEvB,SAASC,GAAkBC,EAAiB,CACjD,OAAOH,EAAe,KAAKI,GAAKA,GAAKD,CAAO,GAAKH,EAAe,GAAG,EAAE,CACvE,CAcO,SAASK,GAAiBC,EAAsC,CACrE,OAAOA,IAAY,SACf,CAAE,QAAAA,EAAS,SAAUP,EAAsB,EAC3C,CAAE,QAAAO,EAAS,SAAUX,EAAqB,CAChD,CAEO,SAASY,GAAmBD,EAAwB,CACzD,OAAOA,IAAY,SAAWR,GAAwBJ,EACxD,CAOA,IAAMc,GAAiE,CACrE,oBAAqB,iCACrB,UAAW,iCACX,UAAW,0BACX,iBAAkB,gCAClB,cAAe,gBACf,eAAgB,8BAChB,KAAM,gCACN,KAAM,gCACN,KAAM,gCACN,KAAM,+CACR,EAEO,SAASC,GAAcC,EAA0C,CACtE,OAAOF,GAAeE,CAAQ,CAChC,CCrIM,SAAUC,EACdC,EACAC,EAAS,OACTC,EAAQ,EAAC,CAET,IAAMC,EAAS,CAACC,EAAYC,KAA6B,CACvD,GAAGD,EACH,GAAAC,EACA,KAAMD,EAAK,MAAQC,EACnB,SAAU,CAAA,IAGNC,EAAOH,EAAOH,EAAM,GAAGC,CAAM,IAAIC,CAAK,EAAE,EACxCK,EAAQ,CAAC,CAAE,IAAKP,EAAM,IAAKM,EAAM,MAAAJ,CAAK,CAAE,EAC9C,KAAOK,EAAM,OAAS,GAAG,CACvB,GAAM,CAAE,IAAAC,EAAK,IAAAC,EAAK,MAAOC,CAAC,EAAKH,EAAM,IAAG,EACxC,GAAIC,EAAI,SAAU,CAChBC,EAAI,SAAWD,EAAI,SAAS,IAAI,CAACG,EAAOC,IACtCT,EAAOQ,EAAO,GAAGF,EAAI,EAAE,IAAIG,CAAC,IAAIF,EAAI,CAAC,EAAE,CAAC,EAE1C,OAAW,CAACE,EAAGD,CAAK,IAAKH,EAAI,SAAS,QAAO,EAC3CD,EAAM,KAAK,CAAE,IAAKI,EAAO,IAAKF,EAAI,SAASG,CAAC,EAAI,MAAOF,EAAI,CAAC,CAAE,CAElE,CACF,CACA,OAAOJ,CACT,CCpCA,IAA8BO,EAA9B,KAAqC,CACzB,KAAO,IAAI,IACb,MACA,MAMR,YAAYC,EAAyC,CACnD,OAAW,CAACC,EAAMC,CAAG,IAAKF,EACnB,KAAK,KAAK,IAAIC,CAAI,GACrB,KAAK,KAAK,IAAIA,EAAMC,CAAG,EAG3B,KAAK,MAAQ,CAAC,GAAG,KAAK,KAAK,KAAI,CAAE,CACnC,CAEA,OAAOD,EAAY,CACjB,OAAO,KAAK,KAAK,IAAIA,CAAI,GAAK,EAChC,CAEA,UAAQ,CACN,OAAO,KAAK,KACd,CAOA,UAAQ,CACN,YAAK,QAAU,KAAK,SAAQ,EAAG,OAC7B,CAACE,EAAKF,IAAS,KAAK,IAAIE,EAAK,KAAK,OAAOF,CAAI,EAAE,MAAM,EACrD,CAAC,EAEI,KAAK,KACd,CAEA,SAAO,CACL,MAAO,CACL,GAAI,OACJ,KAAM,OACN,OAAQ,GACR,SAAU,KAAK,SAAQ,EAAG,IAAIA,IAAS,CACrC,GAAIA,EACJ,SAAU,CAAA,EACV,KAAAA,GACA,EAEN,CAEA,WACEG,EAAa,CAGf,CAEA,eAAa,CACX,MAAO,CAAA,CACT,CAEA,WAAS,CACP,MAAO,CAAA,CACT,CAEA,IAAI,gBAAc,CAChB,MAAO,CAAA,CACT,CAEA,IAAI,cAAY,CAEhB,CAEA,IAAI,6BAA2B,CAE/B,CAEA,IAAI,QAAM,CACR,MAAO,CAAA,CACT,GClEY,SAAPC,EAAuBC,EAAS,CACrC,OAAOC,EAAYD,EAAG,CAAE,iBAAkB,MAAM,CAAE,CACpD,CCHA,SAASE,GAAe,CACtB,MAAO,CACL,GAAI,OAAO,OAAO,IAAI,EACtB,GAAI,OAAO,OAAO,IAAI,EACtB,GAAI,OAAO,OAAO,IAAI,EACtB,GAAI,OAAO,OAAO,IAAI,EACtB,QAAS,CAAA,EACT,QAAS,OAAO,OAAO,IAAI,EAE/B,CAIA,SAASC,EACPC,EACAC,EAAe,CAEf,GAAID,EACF,OAAOA,EAET,GAAIC,EACF,MAAM,IAAI,MAAM,mCAAmC,EAErD,OAAOH,EAAe,CACxB,CAEA,IAAMI,EAAmB,mBACnBC,GAAiB,YACjBC,GAAU,4BACVC,GAAU,4BACVC,GAAU,oCACVC,GAAU,oCAIVC,GAAY,8BACZC,GAAgB,KAEhB,SAAUC,EAAMC,EAAY,CAChC,OAAOT,EAAiB,KAAKS,CAAI,CACnC,CAEM,SAAUC,EACdD,EACAE,EAA2B,CAE3B,IAAMC,EAAUD,GAAQ,CAAA,EAClBE,EAAsB,CAAA,EACxBf,EAA8B,KAG9BgB,EAAgB,GAEdC,EAAQN,EAAK,MAAM;CAAI,EAC7B,QAAWO,KAAQD,EAAO,CACxB,IAAIE,EAEJ,GAAIjB,EAAiB,KAAKgB,CAAI,EACxBlB,GACFe,EAAG,KAAKf,CAAK,EAEfA,EAAQF,EAAe,EACvBkB,EAAgB,WACPb,GAAe,KAAKe,CAAI,EAC7BlB,GACFe,EAAG,KAAKf,CAAK,EAEfA,EAAQ,aACEmB,EAAQf,GAAQ,KAAKc,CAAI,EAAI,CACvClB,EAAQD,EAAYC,EAAO,CAAC,CAACc,EAAQ,MAAM,EAC3C,IAAMM,EAAMD,EAAM,CAAC,EACbE,EAAUrB,EAAM,GAAGoB,CAAG,IAAM,CAAA,EAC9BA,IAAQ,MAAQJ,GAAiBK,EAAO,OAAS,EACnDA,EAAOA,EAAO,OAAS,CAAC,GAAKF,EAAM,CAAC,EAEpCE,EAAO,KAAKF,EAAM,CAAC,CAAE,EAEvBH,EAAgBI,IAAQ,IAC1B,SAAYD,EAAQd,GAAQ,KAAKa,CAAI,EACnClB,EAAQD,EAAYC,EAAO,CAAC,CAACc,EAAQ,MAAM,EAC3Cd,EAAM,GAAGmB,EAAM,CAAC,CAAE,GAAKnB,EAAM,GAAGmB,EAAM,CAAC,CAAE,GAAK,IAAMA,EAAM,CAAC,UACjDA,EAAQb,GAAQ,KAAKY,CAAI,EAAI,CACvClB,EAAQD,EAAYC,EAAO,CAAC,CAACc,EAAQ,MAAM,EAC3C,IAAMQ,EAAUtB,EAAM,GAAGmB,EAAM,CAAC,CAAE,IAAM,OAAO,OAAO,IAAI,GACxDG,EAAOH,EAAM,CAAC,CAAE,IAAM,CAAA,GAAI,KAAKA,EAAM,CAAC,CAAE,CAC5C,SAAYA,EAAQZ,GAAQ,KAAKW,CAAI,EAAI,CACvClB,EAAQD,EAAYC,EAAO,CAAC,CAACc,EAAQ,MAAM,EAC3C,IAAMQ,EAAUtB,EAAM,GAAGmB,EAAM,CAAC,CAAE,IAAM,OAAO,OAAO,IAAI,EAC1DG,EAAOH,EAAM,CAAC,CAAE,GAAKG,EAAOH,EAAM,CAAC,CAAE,GAAK,IAAMA,EAAM,CAAC,CACzD,SAAYA,EAAQX,GAAU,KAAKU,CAAI,EAAI,CACzClB,EAAQD,EAAYC,EAAO,CAAC,CAACc,EAAQ,MAAM,EAC3C,IAAMS,EAAUJ,EAAM,CAAC,EACjBK,EAAUL,EAAM,CAAC,EACnBnB,EAAM,QAAQuB,CAAO,IAAM,SAC7BvB,EAAM,QAAQuB,CAAO,EAAI,GACzBvB,EAAM,QAAQ,KAAKuB,CAAO,GAE5BvB,EAAM,QAAQuB,CAAO,GAAKC,CAC5B,SAAWf,GAAc,KAAKS,CAAI,GAC5BJ,EAAQ,OACV,MAAM,IAAI,MAAM,gBAAgB,CAGtC,CAEA,OAAId,GACFe,EAAG,KAAKf,CAAK,EAGRe,CACT,CCrHA,IAAqBU,EAArB,cAA0CC,CAAO,CACvC,KACA,IAER,YAAYC,EAAcC,EAAwB,CAChD,IAAMC,EAAMC,EAASH,CAAI,EACnBI,EAAMF,EAAID,CAAgB,GAAKC,EAAI,CAAC,EAC1C,GAAI,CAACE,EACH,MAAM,IAAI,MAAM,uCAAuC,EAEzD,MAAMA,EAAI,QAAQ,IAAIC,GAAQ,CAACA,EAAMD,EAAI,QAAQC,CAAI,GAAK,EAAE,CAAC,CAAC,EAC9D,KAAK,KAAOH,EACZ,KAAK,IAAME,CACb,CAEA,QAAM,CACJ,OAAO,KAAK,GACd,CAEA,IAAI,gBAAc,CAChB,OAAO,KAAK,KAAK,IAAI,CAACA,EAAKE,IAAQF,EAAI,GAAG,KAAK,CAAC,GAAK,aAAaE,EAAM,CAAC,EAAE,CAC7E,CAEA,WAAS,CACP,IAAMC,EAAY,KAAK,IAAI,GAAG,IAAM,CAAA,EAC9BC,EAAY,KAAK,IAAI,GAAG,IAAM,CAAA,EACpC,MAAO,CACL,QAAS,KAAK,IAAI,GAClB,WAAY,OAAO,YACjB,OAAO,QAAQD,CAAS,EAAE,IAAI,CAAC,CAACE,EAAGC,CAAC,IAAM,CAACD,EAAGC,EAAE,CAAC,CAAC,CAAC,CAAC,EAEtD,OAAQ,OAAO,YACb,OAAO,QAAQF,CAAS,EAAE,IAAI,CAAC,CAACC,EAAGC,CAAC,IAAM,CAACD,EAAGC,EAAE,KAAK,IAAI,CAAC,CAAC,CAAC,EAGlE,CAEA,WAAWC,EAAe,CACxB,MAAO,CACL,KAAMA,EACN,UAAW,KAAK,IAAI,GAAG,KAAKA,CAAO,IAAI,CAAC,EACxC,OAAQ,KAAK,IAAI,GAAG,KAAKA,CAAO,GAAG,KAAK,IAAI,EAEhD,CAEA,eAAa,CACX,IAAMC,EAAW,iDACXJ,EAAY,KAAK,IAAI,GAAG,IAAM,CAAA,EAC9BK,EAGF,CAAA,EACJ,OAAW,CAACC,EAAIC,CAAM,IAAK,OAAO,QAAQP,CAAS,EACjD,QAAWQ,KAAMD,EAAQ,CACvB,IAAME,EAAQL,EAAS,KAAKI,CAAE,EAC1BC,IACAJ,EAAOC,CAAE,IAAM,CAAA,GAAI,KAAK,CACxB,IAAKG,EAAM,CAAC,EAAG,YAAW,EAC1B,MAAOA,EAAM,CAAC,EACd,SAAU,CAACA,EAAM,CAAC,EAClB,OAAQ,CAACA,EAAM,CAAC,EACjB,CAEL,CAEF,OAAOJ,CACT,CAEA,SAAO,CACL,IAAMK,EAAO,KAAK,IAAI,GAAG,KAAK,CAAC,EAC/B,OAAOA,EAAOC,EAAgBC,EAAYF,CAAI,CAAC,EAAI,MAAM,QAAO,CAClE,CAEA,IAAI,cAAY,CACd,OAAO,KAAK,IAAI,GAAG,QACrB,CAEA,IAAI,6BAA2B,CAC7B,OAAO,KAAK,IAAI,GAAG,OACrB,CAOA,IAAI,QAAM,CACR,GAAM,CAAE,SAAAG,EAAU,QAAAC,EAAS,GAAGC,CAAO,EAAK,KAAK,IAAI,GACnD,MAAO,CACL,CACE,GAAI,eACJ,KAAM,qBACN,KAAMF,EACN,kBAAmB,CAAA,GAErB,CACE,GAAI,kBACJ,KAAM,sBACN,KAAMC,EACN,kBAAmBE,GAErB,GAAG,OAAO,QAAQD,CAAO,EAAE,IAAI,CAAC,CAACE,EAAKC,CAAI,KAAO,CAC/C,GAAI,MAAMD,CAAG,GACb,KAAMA,EACN,KAAAC,EACA,kBAAmBC,EAAgBF,CAAG,GACtC,EACF,GAAG,OAAO,QAAQ,KAAK,IAAI,EAAE,EAAE,QAAQ,CAAC,CAACA,EAAKG,CAAK,IACjD,OAAO,QAAQA,CAAK,EAAE,IAAI,CAAC,CAACC,EAAKH,CAAI,KAAO,CAC1C,GAAI,MAAMG,CAAG,IAAIJ,CAAG,GACpB,KAAM,GAAGI,CAAG,IAAIJ,CAAG,GACnB,KAAAC,EACA,kBAAmBC,EAAgBF,CAAG,EACtC,WAAY,IACZ,CAAC,EAGT,GAMID,EAAqC,CACzC,IAAK,YACL,IAAK,YACL,IAAK,YACL,IAAK,YACL,IAAK,OACL,IAAK,OACL,IAAK,OACL,IAAK,QAIP,SAASG,EAAgBF,EAAW,CAClC,OAAOA,IAAQ,MAAQA,EAAI,SAAS,KAAK,EAAID,EAAa,CAAA,CAC5D,CC3IM,SAAUM,EAAWC,EAAY,CACrC,MAAO,aAAa,KAAKA,CAAI,CAC/B,CAaM,SAAUC,EAAkBD,EAAY,CAC5C,IAAME,EAAyB,CAAA,EACzBC,EAAO,IAAI,IACbC,EAEEC,EAAQ,IAAK,CACbD,GAAW,CAACD,EAAK,IAAIC,EAAQ,EAAE,IACjCD,EAAK,IAAIC,EAAQ,EAAE,EACnBF,EAAQ,KAAK,CACX,GAAIE,EAAQ,GACZ,IAAKA,EAAQ,MAAM,KAAK,EAAE,EAAE,WAAW,MAAO,EAAE,EACjD,EAEL,EAEIE,EAAQ,EACZ,QAAWC,KAAQP,EAAK,MAAM;CAAI,EAC5BO,EAAK,WAAW,GAAG,GACrBF,EAAK,EACLC,IAEAF,EAAU,CAAE,GADD,aAAa,KAAKG,CAAI,EAAG,CAAC,GAAK,WAAWD,CAAK,GAC1C,MAAO,CAAA,CAAE,GAEzBF,GAAS,MAAM,KAAKG,CAAI,EAG5B,OAAAF,EAAK,EAEEH,CACT,CAEM,SAAUM,EAAUC,EAA6B,CACrD,OAAO,OAAOA,GAAU,SAAWR,EAAkBQ,CAAK,EAAIA,CAChE,CC3BA,IAAMC,GAAS,GACTC,GAAS,GACTC,GAAS,GACTC,GAAS,IACTC,GAAY,GAElB,SAASC,EAAQC,EAAY,CAC3B,OAAOA,GAAQJ,IAAUI,GAAQH,EACnC,CAEA,SAASI,EAAQD,EAAY,CAC3B,OAAQA,GAAQN,IAAUM,GAAQL,IAAWK,IAASF,EACxD,CAYA,SAASI,GAASC,EAAW,CAC3B,IAAMC,EAAoB,CAAA,EACpBC,EAAU,CAAC,EAAE,EAEnB,QAAWC,KAAMH,EAAK,CACpB,IAAMH,EAAOM,EAAG,WAAW,CAAC,EACxBL,EAAQD,CAAI,GACdI,EAAQ,KAAKE,CAAE,EACfD,EAAQ,KAAK,EAAE,GACNN,EAAQC,CAAI,IACrBK,EAAQA,EAAQ,OAAS,CAAC,GAAKC,EAAG,YAAW,EAIjD,CAEA,MAAO,CAAE,QAAAF,EAAS,QAAAC,CAAO,CAC3B,CAEA,IAAqBE,EAArB,cAAoCC,CAAO,CACzC,YAAYC,EAA6B,CACvC,IAAMC,EAAUC,EAAUF,CAAK,EACzBG,EAAWC,GAAUH,EAAQ,IAAII,GAAKA,EAAE,GAAG,CAAC,EAClD,MAAMJ,EAAQ,IAAI,CAACI,EAAGC,IAAM,CAACD,EAAE,GAAIF,EAASG,CAAC,CAAE,CAAC,CAAC,CACnD,CAEA,OAAO,MAAMN,EAA6B,CACxC,GAAI,OAAOA,GAAU,UAAY,CAACO,EAAWP,CAAK,EAChD,MAAO,GAGT,IAAMQ,EAAON,EAAUF,CAAK,EACzB,IAAIK,GAAKA,EAAE,GAAG,EACd,OAAOI,GAAK,CAAC,CAACA,CAAC,EAWlB,GATID,EAAK,OAAS,GASd,IAAI,IAAIA,EAAK,IAAIC,GAAKA,EAAE,MAAM,CAAC,EAAE,OAAS,EAC5C,MAAO,GAGT,IAAIC,EAAe,GACfC,EACJ,QAAWjB,KAAOc,EAAM,CACtB,IAAIb,EAAU,EACd,QAAS,EAAI,EAAG,EAAID,EAAI,OAAQ,IAAK,CACnC,IAAMH,EAAOG,EAAI,WAAW,CAAC,EACzBF,EAAQD,CAAI,EACdI,IACSL,EAAQC,CAAI,IACrBmB,EAAe,GAEnB,CACA,GAAIC,IAAe,QAAahB,IAAYgB,EAC1C,MAAO,GAETA,EAAahB,CACf,CACA,OAAOe,CACT,GAQF,SAASN,GAAUQ,EAAiB,CAClC,IAAMC,EAAOD,EAAQ,IAAInB,EAAQ,EAI7BqB,EAAe,EACnB,OAAW,CAAE,QAAAnB,CAAO,IAAMkB,EACxBC,EAAe,KAAK,IAAIA,EAAcnB,EAAQ,MAAM,EAItD,IAAMoB,EAAa,IAAI,MAAcD,EAAe,CAAC,EAAE,KAAK,CAAC,EAC7D,OAAW,CAAE,QAAAlB,CAAO,IAAMiB,EACxB,OAAW,CAACG,EAAKC,CAAG,IAAKrB,EAAQ,QAAO,EACtCmB,EAAWC,CAAG,EAAI,KAAK,IAAID,EAAWC,CAAG,EAAIC,EAAI,MAAM,EAI3D,OAAOJ,EAAK,IAAI,CAAC,CAAE,QAAAlB,EAAS,QAAAC,CAAO,IAAM,CACvC,IAAMsB,EAAmB,CAAA,EACzB,QAASF,EAAM,EAAGA,GAAOF,EAAcE,IAAO,CAC5C,IAAMC,EAAMrB,EAAQoB,CAAG,GAAK,GAC5BE,EAAO,KAAKD,EAAK,IAAI,OAAOF,EAAWC,CAAG,EAAKC,EAAI,MAAM,CAAC,EACtDD,EAAMF,GAERI,EAAO,KAAKvB,EAAQqB,CAAG,GAAK,GAAG,CAEnC,CACA,OAAOE,EAAO,KAAK,EAAE,CACvB,CAAC,CACH,CCvJA,IAAqBC,EAArB,cAAwCC,CAAO,CACrC,IAER,YAAYC,EAAY,CACtB,IAAMC,EAAMC,EAAMF,CAAI,EACtB,MAAMC,EAAI,KAAK,IAAIE,GAAO,CAACA,EAAI,GAAIA,EAAI,GAAG,CAAC,CAAC,EAC5C,KAAK,IAAMF,CACb,CAEA,WAAS,CACP,OAAO,KAAK,IAAI,MAClB,CAEA,IAAI,cAAY,CACd,OAAO,KAAK,IAAI,SAClB,GCfF,IAAqBG,EAArB,cAAoCC,CAAO,CACzC,YAAYC,EAAY,CACtB,MAAMC,EAAYD,CAAI,EAAE,IAAIE,GAAO,CAACA,EAAI,QAASA,EAAI,GAAG,CAAC,CAAC,CAC5D,GCFF,IAAqBC,EAArB,cAAsCC,CAAO,CAEnC,gBAAkB,IAAI,IAE9B,YAAYC,EAA6B,CACvC,IAAMC,EAAUC,EAAUF,CAAK,EAC/B,MAAMC,EAAQ,IAAIE,GAAK,CAACA,EAAE,GAAIA,EAAE,GAAG,CAAC,CAAC,EACrC,OAAW,CAAE,GAAAC,CAAE,IAAMH,EACfG,EAAG,SAAS,GAAG,GACjB,KAAK,gBAAgB,IAAIA,EAAG,WAAW,IAAK,GAAG,EAAGA,CAAE,CAG1D,CAEA,OAAOC,EAAY,CACjB,OACE,KAAK,KAAK,IAAIA,CAAI,GAClB,KAAK,KAAK,IAAI,KAAK,gBAAgB,IAAIA,CAAI,GAAK,EAAE,GAClD,EAEJ,GCNF,IAAMC,GAAW,iCACXC,GAAgB,8CAIhB,SAAUC,GACdC,EACAC,EAAmB,EACnBC,EAAkB,CAElB,IAAMC,EAAOH,EACV,QAAQ,UAAW,EAAE,EACrB,WAAW,SAAU;CAAI,EACzB,UAAS,EACZ,GAAIH,GAAS,KAAKM,CAAI,EACpB,MAAM,IAAI,MACR,uFAAuF,EAG3F,GAAID,IAAW,YACb,OAAO,IAAIE,EAAaD,EAAMF,CAAgB,EAEhD,GAAIC,IAAW,MACb,OAAO,IAAIG,EAAOF,CAAI,EAExB,GAAID,IAAW,QACb,OAAO,IAAII,EAASH,CAAI,EAE1B,GAAID,IAAW,MACb,OAAO,IAAIK,EAAOJ,CAAI,EAExB,GAAID,IAAW,UACb,OAAO,IAAIM,EAAWL,CAAI,EAE5B,GAAIM,EAAeN,CAAI,EACrB,OAAO,IAAIC,EAAaD,EAAMF,CAAgB,EAEhD,GAAIS,EAAWP,CAAI,EAAG,CACpB,IAAMQ,EAAUC,EAAkBT,CAAI,EACtC,OAAOE,EAAO,MAAMM,CAAO,EAAI,IAAIN,EAAOM,CAAO,EAAI,IAAIL,EAASK,CAAO,CAC3E,CACA,GAAIR,EAAK,WAAW,KAAK,EACvB,OAAO,IAAII,EAAOJ,CAAI,EAExB,GAAIL,GAAc,KAAKK,CAAI,EACzB,OAAO,IAAIK,EAAWL,CAAI,EAE5B,IAAMU,EAAYV,EAAK,MAAM;EAAM,CAAC,EAAE,CAAC,EAAG,MAAM,EAAG,EAAE,EACrD,MAAM,IAAI,MACRU,EACI,4GAA4GA,CAAS,IACrH,6BAA6B,CAErC,CAKM,SAAUC,GAAoBC,EAAkB,CACpD,OAAOA,EAAW,WAAW,QAAS,EAAE,CAC1C",
+  "names": ["hostOf", "url", "HttpError", "message", "status", "handleFetch", "args", "response", "e", "textfetch", "jsonfetch", "timeout", "time", "signal", "resolve", "reject", "onAbort", "id", "isAbortError", "import_react", "readLocalStorage", "key", "initialValue", "item", "error", "useLocalStorage", "storedValue", "setStoredValue", "value", "pollLoop", "check", "intervalSeconds", "onCountdown", "signal", "i", "timeout", "EBI_BASE", "EBI_EMAIL_STORAGE_KEY", "DEFAULT_EBI_EMAIL", "getEbiEmail", "readLocalStorage", "FAILED_STATUSES", "submitEbiJob", "tool", "params", "signal", "textfetch", "STATUS_FAILURE_BUDGET_MS", "waitForEbiJob", "jobId", "intervalSeconds", "onCountdown", "failingSince", "pollLoop", "status", "e", "isAbortError", "runEbiJob", "label", "onProgress", "onRid", "s", "type", "BASE_BLAST_URL", "ebiMsaAlgorithms", "msaAlgorithms", "msaAlgorithmLabels", "blastDatabaseOptions", "defaultBlastDatabase", "searchPrograms", "searchProgramLabels", "phmmerDatabaseOptions", "defaultPhmmerDatabase", "blastHitCounts", "defaultMaxHits", "snapBlastHitCount", "maxHits", "n", "defaultSearchFor", "program", "databaseOptionsFor", "databaseLabels", "databaseLabel", "database", "generateNodeIds", "tree", "parent", "depth", "withId", "node", "id", "root", "stack", "src", "out", "d", "child", "i", "BaseMSA", "rows", "name", "seq", "max", "_name", "parse", "s", "parseNewick", "createStockholm", "ensureStock", "stock", "strict", "formatStartRegex", "formatEndRegex", "gfRegex", "gcRegex", "gsRegex", "grRegex", "lineRegex", "nonwhiteRegex", "sniff", "text", "parseAll", "opts", "options", "db", "treeContinues", "lines", "line", "match", "tag", "values", "byName", "seqname", "seqdata", "StockholmMSA", "BaseMSA", "text", "currentAlignment", "res", "parseAll", "aln", "name", "idx", "acEntries", "drEntries", "k", "v", "rowName", "pdbRegex", "result", "id", "drList", "dr", "match", "tree", "generateNodeIds", "parse", "seq_cons", "SS_cons", "otherGc", "wussColors", "tag", "data", "structureColors", "byRow", "row", "fastaSniff", "text", "splitFastaRecords", "records", "seen", "current", "flush", "count", "line", "toRecords", "input", "CODE_A", "CODE_Z", "CODE_a", "CODE_z", "CODE_DASH", "isLower", "code", "isMatch", "parseRow", "seq", "matches", "inserts", "ch", "A3mMSA", "BaseMSA", "input", "records", "toRecords", "expanded", "expandA3M", "r", "i", "fastaSniff", "seqs", "s", "hasLowercase", "matchCount", "rawSeqs", "rows", "numPositions", "maxInserts", "pos", "ins", "result", "ClustalMSA", "BaseMSA", "text", "msa", "parse", "aln", "EmfMSA", "BaseMSA", "text", "parseEmfAln", "aln", "FastaMSA", "BaseMSA", "input", "records", "toRecords", "r", "id", "name", "htmlPage", "clustalHeader", "parseMSA", "input", "currentAlignment", "format", "text", "StockholmMSA", "A3mMSA", "FastaMSA", "EmfMSA", "ClustalMSA", "sniff", "fastaSniff", "records", "splitFastaRecords", "firstLine", "getUngappedSequence", "alignedSeq"]
+}

package/dist/chunks/{chunk-NI3VGKQP.js → chunk-BAM67QHH.js}

@@ -1,3 +1,3 @@
-import{a as H,c as J,d as S,e as Q,f as Z,p as Y}from"./chunk-F726IWCW.js";import{a as Pe}from"./chunk-IBBQUV2I.js";import{a as Ne}from"./chunk-2IWD4OO4.js";import{a as Te,b as K}from"./chunk-FY3BTKY4.js";var Re=Te((bt,oe)=>{oe.exports=JBrowseExports["@jbrowse/core/util/translateTranscript"]});var M=K(Pe());function ut(e){return(0,M.getContainingView)(e)}function te(e){return typeof e=="string"&&e!==""}function ne(e){return[...new Set(e.filter(te))]}function re(e,t){return t.filter(te).join(e)}function Ee(e){let n=(e.get("subfeatures")??[]).filter(r=>(r.get("type")==="mRNA"||r.get("type")==="transcript")&&r.get("subfeatures")?.some(o=>o.get("type")==="CDS"));return n.length>0?n:[e]}function ee(e){let t=(0,M.sum)(e.get("subfeatures")?.filter(n=>n.get("type")==="CDS").map(n=>n.get("end")-n.get("start"))??[]);return{len:Math.floor(t/3),mod:t%3}}function mt(e){return e?.id()??""}function Me(e){return e?ne([e.id(),e.get("name"),e.get("id"),e.get("transcript_id")]):[]}function dt(e,t){return Me(e).includes(t)}function Ae(e){return e?re(" ",[e.get("name"),e.get("id")]):""}function _e(e){return e?re(" ",[e.get("gene_name")??e.get("name"),e.get("id")?`(${e.get("id")})`:void 0]):""}function lt(e,t){return`BLAST - ${_e(e)} - ${Ae(t)}`}function gt(e){return Ee(e).toSorted((n,r)=>ee(r).len-ee(n).len)}function ft(e){return e.replace(/[*&]+$/,"").replaceAll(/[*&]/g,"X")}function ht(e){return ne([e.id(),e.get("id"),e.get("name"),e.get("gene_id"),e.get("gene_name")])}var se=K(Ne());async function xt({start:e,end:t,refName:n,session:r,assemblyName:o}){let{assemblyManager:a,rpcManager:i}=r,c=await a.waitForAssembly(o);if(!c)throw new Error("assembly not found");return{seq:(await i.call("getSequence","CoreGetFeatures",{adapterConfig:(0,se.getConf)(c,["sequence","adapter"]),regions:[{start:e,end:t,refName:c.getCanonicalRefName(n)??n,assemblyName:o}]}))[0]?.get("seq")??"",assemblyGeneticCodeId:c.getGeneticCodeId(n)}}var $e="jbrowse-plugin-msaview",Oe="jbrowse2@berkeley.edu",ae="https://eutils.ncbi.nlm.nih.gov/entrez/eutils";function ce(e){return new URLSearchParams({...e,tool:$e,email:Oe})}function L(e,t){return`${ae}/${e}.fcgi?${ce(t).toString()}`}function _(e){return L("efetch",e)}function ue(e){return[`${ae}/efetch.fcgi`,{method:"POST",body:ce(e)}]}var ie=350,A=0;async function me(e){let t=Date.now(),n=Math.max(t,A);if(A=n+ie,n>t)try{await Q(n-t,e??void 0)}catch(r){throw A===n+ie&&(A=n),r}}async function B(e,t){return await me(t?.signal),J(e,t)}async function de(e,t){return await me(t?.signal),S(e,t)}var je={amp:"&",apos:"'",gt:">",lt:"<",quot:'"'};function k(e){return e.replaceAll(/&(#x[\da-f]+|#\d+|[a-z]+);/gi,(t,n)=>n.startsWith("#x")||n.startsWith("#X")?String.fromCodePoint(Number.parseInt(n.slice(2),16)):n.startsWith("#")?String.fromCodePoint(Number(n.slice(1))):je[n]??t)}var F="https://api.ncbi.nlm.nih.gov/datasets/v2",Le=100;function ke(e){return e.trim().replace(/^\w+:/,"").replace(/\.\d+$/,"")}function Fe(e,t){let n=e.toLowerCase();return(t.find(o=>o.symbol===e)??t.find(o=>o.synonyms?.includes(e))??t.find(o=>o.symbol?.toLowerCase()===n)??t[0])?.gene_id}async function ve(e,t,n){try{return((await S(`${F}/gene/symbol/${encodeURIComponent(e)}/taxon/${t}`,{signal:n})).reports??[]).flatMap(o=>o.gene?[o.gene]:[])}catch(r){if(r instanceof H&&(r.status===400||r.status===404))return[];throw r}}async function Ge(e,t,n){return(await de(L("esearch",{db:"gene",term:`${e}[Gene Name] AND ${t}[taxid]`,retmode:"json",retmax:"1"}),{signal:n})).esearchresult?.idlist?.[0]}async function Bt(e,t,n){let r=new Set,o=e.map(c=>c.trim()),a=c=>/^\d+$/.test(c);for(let c of o.filter(s=>!a(s))){let s=ke(c);if(!s||r.has(s))continue;r.add(s);let u=Fe(s,await ve(s,t,n))??await Ge(s,t,n);if(u)return{geneId:u,matched:s}}let i=o.find(a);return i?{geneId:i,matched:i}:void 0}async function Ve(e,{taxa:t,exclude:n,limit:r=Le,signal:o}={}){let a=await S(`${F}/gene/id/${e}/orthologs?returned_content=COMPLETE`,{signal:o}),i=new Map;for(let{gene:c}of a.reports??[]){let s=Number(c?.tax_id);if(c?.gene_id&&s!==n&&(t?.has(s)??!0)&&!i.has(s)&&i.set(s,{taxId:s,geneId:c.gene_id,scientificName:c.taxname??String(s),commonName:c.common_name}),i.size>=r)break}return[...i.values()]}var le=150;async function ge(e,t){let n=new Map;for(let r=0;r<e.length;r+=le){let o=e.slice(r,r+le),a=await S(`${F}/gene/id/${o.join(",")}/product_report?page_size=${o.length}`,{signal:t});for(let{product:i}of a.reports??[]){let c=(i?.transcripts??[]).map(u=>({acc:u.protein?.accession_version,len:u.protein?.length??0,mane:/select/i.test(u.select_category??"")})).filter(u=>!!u.acc),s=c.find(u=>u.mane)??[...c].sort((u,d)=>d.len-u.len).at(0);i?.gene_id&&s&&n.set(i.gene_id,s.acc)}}return n}function fe(e){let t=new Map,n,r=[];for(let o of e.split(`
+import{a as H,c as J,d as S,e as Q,f as Z,p as Y}from"./chunk-A63PUWQZ.js";import{a as Pe}from"./chunk-IBBQUV2I.js";import{a as Ne}from"./chunk-2IWD4OO4.js";import{a as Te,b as K}from"./chunk-FY3BTKY4.js";var Re=Te((bt,oe)=>{oe.exports=JBrowseExports["@jbrowse/core/util/translateTranscript"]});var M=K(Pe());function ut(e){return(0,M.getContainingView)(e)}function te(e){return typeof e=="string"&&e!==""}function ne(e){return[...new Set(e.filter(te))]}function re(e,t){return t.filter(te).join(e)}function Ee(e){let n=(e.get("subfeatures")??[]).filter(r=>(r.get("type")==="mRNA"||r.get("type")==="transcript")&&r.get("subfeatures")?.some(o=>o.get("type")==="CDS"));return n.length>0?n:[e]}function ee(e){let t=(0,M.sum)(e.get("subfeatures")?.filter(n=>n.get("type")==="CDS").map(n=>n.get("end")-n.get("start"))??[]);return{len:Math.floor(t/3),mod:t%3}}function mt(e){return e?.id()??""}function Me(e){return e?ne([e.id(),e.get("name"),e.get("id"),e.get("transcript_id")]):[]}function dt(e,t){return Me(e).includes(t)}function Ae(e){return e?re(" ",[e.get("name"),e.get("id")]):""}function _e(e){return e?re(" ",[e.get("gene_name")??e.get("name"),e.get("id")?`(${e.get("id")})`:void 0]):""}function lt(e,t){return`BLAST - ${_e(e)} - ${Ae(t)}`}function gt(e){return Ee(e).toSorted((n,r)=>ee(r).len-ee(n).len)}function ft(e){return e.replace(/[*&]+$/,"").replaceAll(/[*&]/g,"X")}function ht(e){return ne([e.id(),e.get("id"),e.get("name"),e.get("gene_id"),e.get("gene_name")])}var se=K(Ne());async function xt({start:e,end:t,refName:n,session:r,assemblyName:o}){let{assemblyManager:a,rpcManager:i}=r,c=await a.waitForAssembly(o);if(!c)throw new Error("assembly not found");return{seq:(await i.call("getSequence","CoreGetFeatures",{adapterConfig:(0,se.getConf)(c,["sequence","adapter"]),regions:[{start:e,end:t,refName:c.getCanonicalRefName(n)??n,assemblyName:o}]}))[0]?.get("seq")??"",assemblyGeneticCodeId:c.getGeneticCodeId(n)}}var $e="jbrowse-plugin-msaview",Oe="jbrowse2@berkeley.edu",ae="https://eutils.ncbi.nlm.nih.gov/entrez/eutils";function ce(e){return new URLSearchParams({...e,tool:$e,email:Oe})}function L(e,t){return`${ae}/${e}.fcgi?${ce(t).toString()}`}function _(e){return L("efetch",e)}function ue(e){return[`${ae}/efetch.fcgi`,{method:"POST",body:ce(e)}]}var ie=350,A=0;async function me(e){let t=Date.now(),n=Math.max(t,A);if(A=n+ie,n>t)try{await Q(n-t,e??void 0)}catch(r){throw A===n+ie&&(A=n),r}}async function B(e,t){return await me(t?.signal),J(e,t)}async function de(e,t){return await me(t?.signal),S(e,t)}var je={amp:"&",apos:"'",gt:">",lt:"<",quot:'"'};function k(e){return e.replaceAll(/&(#x[\da-f]+|#\d+|[a-z]+);/gi,(t,n)=>n.startsWith("#x")||n.startsWith("#X")?String.fromCodePoint(Number.parseInt(n.slice(2),16)):n.startsWith("#")?String.fromCodePoint(Number(n.slice(1))):je[n]??t)}var F="https://api.ncbi.nlm.nih.gov/datasets/v2",Le=100;function ke(e){return e.trim().replace(/^\w+:/,"").replace(/\.\d+$/,"")}function Fe(e,t){let n=e.toLowerCase();return(t.find(o=>o.symbol===e)??t.find(o=>o.synonyms?.includes(e))??t.find(o=>o.symbol?.toLowerCase()===n)??t[0])?.gene_id}async function ve(e,t,n){try{return((await S(`${F}/gene/symbol/${encodeURIComponent(e)}/taxon/${t}`,{signal:n})).reports??[]).flatMap(o=>o.gene?[o.gene]:[])}catch(r){if(r instanceof H&&(r.status===400||r.status===404))return[];throw r}}async function Ge(e,t,n){return(await de(L("esearch",{db:"gene",term:`${e}[Gene Name] AND ${t}[taxid]`,retmode:"json",retmax:"1"}),{signal:n})).esearchresult?.idlist?.[0]}async function Bt(e,t,n){let r=new Set,o=e.map(c=>c.trim()),a=c=>/^\d+$/.test(c);for(let c of o.filter(s=>!a(s))){let s=ke(c);if(!s||r.has(s))continue;r.add(s);let u=Fe(s,await ve(s,t,n))??await Ge(s,t,n);if(u)return{geneId:u,matched:s}}let i=o.find(a);return i?{geneId:i,matched:i}:void 0}async function Ve(e,{taxa:t,exclude:n,limit:r=Le,signal:o}={}){let a=await S(`${F}/gene/id/${e}/orthologs?returned_content=COMPLETE`,{signal:o}),i=new Map;for(let{gene:c}of a.reports??[]){let s=Number(c?.tax_id);if(c?.gene_id&&s!==n&&(t?.has(s)??!0)&&!i.has(s)&&i.set(s,{taxId:s,geneId:c.gene_id,scientificName:c.taxname??String(s),commonName:c.common_name}),i.size>=r)break}return[...i.values()]}var le=150;async function ge(e,t){let n=new Map;for(let r=0;r<e.length;r+=le){let o=e.slice(r,r+le),a=await S(`${F}/gene/id/${o.join(",")}/product_report?page_size=${o.length}`,{signal:t});for(let{product:i}of a.reports??[]){let c=(i?.transcripts??[]).map(u=>({acc:u.protein?.accession_version,len:u.protein?.length??0,mane:/select/i.test(u.select_category??"")})).filter(u=>!!u.acc),s=c.find(u=>u.mane)??[...c].sort((u,d)=>d.len-u.len).at(0);i?.gene_id&&s&&n.set(i.gene_id,s.acc)}}return n}function fe(e){let t=new Map,n,r=[];for(let o of e.split(`
 `))o.startsWith(">")?(n&&t.set(n,r.join("")),n=o.slice(1).split(/\s+/)[0],r=[]):r.push(o.trim());return n&&t.set(n,r.join("")),t}function qe(e){return e.replace(/[^A-Za-z0-9]+/g,"_").replace(/^_+|_+$/g,"")}function Ue(e){let t=new Set;return e.map(n=>{let r=qe(n)||"row",o=r,a=1;for(;t.has(o);)a+=1,o=`${r}_${a}`;return t.add(o),o})}async function Ct(e,t){let n=(await ge([e],t)).get(e);if(!n)return;let r=fe(await B(_({db:"protein",id:n,rettype:"fasta",retmode:"text"}),{signal:t})).get(n);return r?{accession:n,sequence:r}:void 0}async function Tt({geneId:e,taxa:t,exclude:n,limit:r,onProgress:o,signal:a}){o("Finding orthologs across species...");let i=await Ve(e,{taxa:t,exclude:n,limit:r,signal:a});if(i.length<2)throw new Error(`Only ${i.length} ortholog(s) found for this gene \u2014 not enough to align`);o("Selecting a representative protein per species...");let c=await ge(i.map(m=>m.geneId),a),s=i.filter(m=>c.has(m.geneId));if(s.length<2)throw new Error("Could not resolve representative proteins for the orthologs");o(`Fetching ${s.length} protein sequences...`);let u=s.map(m=>c.get(m.geneId)),[d,h]=ue({db:"protein",id:u.join(","),rettype:"fasta",retmode:"text"}),l=fe(await B(d,{...h,signal:a})),p=Ue(s.map(m=>m.commonName??m.scientificName)),w=s.map((m,b)=>{let g=c.get(m.geneId);return{taxId:m.taxId,label:p[b],scientificName:m.scientificName,commonName:m.commonName,geneId:m.geneId,protein:g,sequence:l.get(g)??""}}).filter(m=>m.sequence);if(w.length<2)throw new Error("Could not fetch protein sequences for the orthologs");return w}var V=(e,t)=>t.some(n=>e instanceof n),he,pe;function We(){return he||(he=[IDBIndex,IDBObjectStore,IDBCursor,IDBDatabase,IDBTransaction])}function ze(){return pe||(pe=["advance","continue","continuePrimaryKey"].map(e=>IDBCursor.prototype[e]))}var q=new WeakMap,v=new WeakMap,R=new WeakMap;function Xe(e){let t=new Promise((n,r)=>{let o=()=>{e.removeEventListener("success",a),e.removeEventListener("error",i)},a=()=>{n(y(e.result)),o()},i=()=>{r(e.error),o()};e.addEventListener("success",a),e.addEventListener("error",i)});return R.set(t,e),t}function Ke(e){if(q.has(e))return;let t=new Promise((n,r)=>{let o=()=>{e.removeEventListener("complete",a),e.removeEventListener("error",i),e.removeEventListener("abort",i)},a=()=>{n(),o()},i=()=>{r(e.error||new DOMException("AbortError","AbortError")),o()};e.addEventListener("complete",a),e.addEventListener("error",i),e.addEventListener("abort",i)});q.set(e,t)}var U={get(e,t,n){if(e instanceof IDBTransaction){if(t==="done")return q.get(e);if(t==="store")return n.objectStoreNames[1]?void 0:n.objectStore(n.objectStoreNames[0])}return y(e[t])},set(e,t,n){return e[t]=n,!0},has(e,t){return e instanceof IDBTransaction&&(t==="done"||t==="store")?!0:t in e}};function ye(e){U=e(U)}function He(e){return ze().includes(e)?function(...t){return e.apply(W(this),t),y(this.request)}:function(...t){return y(e.apply(W(this),t))}}function Je(e){return typeof e=="function"?He(e):(e instanceof IDBTransaction&&Ke(e),V(e,We())?new Proxy(e,U):e)}function y(e){if(e instanceof IDBRequest)return Xe(e);if(v.has(e))return v.get(e);let t=Je(e);return Object.is(t,e)||(v.set(e,t),R.set(t,e)),t}var W=e=>R.get(e);function Se(e,t,{blocked:n,upgrade:r,blocking:o,terminated:a}={}){let i=indexedDB.open(e,t),c=y(i);return r&&i.addEventListener("upgradeneeded",s=>{r(y(i.result),s.oldVersion,s.newVersion,y(i.transaction),s)}),n&&i.addEventListener("blocked",s=>n(s.oldVersion,s.newVersion,s)),c.then(s=>{a&&s.addEventListener("close",()=>a()),o&&s.addEventListener("versionchange",u=>o(u.oldVersion,u.newVersion,u))}).catch(()=>{}),c}var Qe=["get","getKey","getAll","getAllKeys","count"],Ze=["put","add","delete","clear"],G={};function be(e,t){if(!(e instanceof IDBDatabase&&!(t in e)&&typeof t=="string"))return;if(G[t])return G[t];let n=t.replace(/FromIndex$/,""),r=t!==n,o=Ze.includes(n);if(!(n in(r?IDBIndex:IDBObjectStore).prototype)||!(o||Qe.includes(n)))return;let a=async function(i,...c){let s=this.transaction(i,o?"readwrite":"readonly"),u=s.store;return r&&(u=u.index(c.shift())),(await Promise.all([u[n](...c),o&&s.done]))[0]};return G[t]=a}ye(e=>({...e,get:(t,n,r)=>be(t,n)||e.get(t,n,r),has:(t,n)=>!!be(t,n)||e.has(t,n)}));var Ye=["advance","continue","continuePrimaryKey"],xe={},z=new WeakMap,De=new WeakMap,et={get(e,t){if(!Ye.includes(t))return e[t];let n=xe[t];return n||(n=xe[t]=function(...r){z.set(this,De.get(this)[t](...r))}),n}};async function*tt(...e){let t=this;if(t instanceof IDBCursor||(t=await t.openCursor(...e)),!t)return;t=t;let n=new Proxy(t,et);for(De.set(n,t),R.set(n,W(t));t;)yield n,t=await(z.get(n)||t.continue()),z.delete(n)}function we(e,t){return t===Symbol.asyncIterator&&V(e,[IDBIndex,IDBObjectStore,IDBCursor])||t==="iterate"&&V(e,[IDBIndex,IDBObjectStore])}ye(e=>({...e,get(t,n,r){return we(t,n)?tt:e.get(t,n,r)},has(t,n){return we(t,n)||e.has(t,n)}}));function $(e,t,n){let r,o=()=>{r=void 0};return()=>(r??=new Promise((a,i)=>{let c=!1;Se(e,t,{upgrade:n,blocked(s){c=!0,i(new Error(`${e} is held open at version ${s} by another tab`))},blocking(s,u,d){d.target.close(),o()},terminated:o}).then(s=>{c?s.close():a(s)},i)}).catch(a=>{throw o(),a}),r)}async function C(e,t,n){try{return await t()}catch(r){return console.warn(`[msaview] ${e} failed, continuing without it:`,r),n}}var nt="jbrowse-msaview-blast-cache",f="blast-results",rt=2,Ie=50,X=$(nt,rt,(e,t)=>{t<2&&e.objectStoreNames.contains(f)&&e.deleteObjectStore(f),e.objectStoreNames.contains(f)||e.createObjectStore(f,{keyPath:"id"})});function ot({proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,transcriptId:o,maxHits:a}){let i=o?`:${o}`:"",c=a===void 0||a===Y?"":`:n${a}`;return r==="phmmer"?`phmmer:${t}${i}${c}:${e}`:`${t}:${n}${i}${c}:${e}`}function Rt({proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,maxHits:o,msa:a,tree:i,treeMetadata:c,rid:s,geneId:u,transcriptId:d,transcriptName:h,geneName:l}){return C("BLAST history write",async()=>{let p=await X(),w={id:ot({proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,transcriptId:d,maxHits:o}),proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,maxHits:o,msa:a,tree:i,treeMetadata:c,rid:s,timestamp:Date.now(),geneId:u,transcriptId:d,transcriptName:h,geneName:l};return await p.put(f,w),await st(p),w},void 0)}async function st(e){try{if(await e.count(f)<=Ie)return;let t=await e.getAll(f),n=t.toSorted((o,a)=>o.timestamp-a.timestamp).slice(0,t.length-Ie),r=e.transaction(f,"readwrite");await Promise.all([...n.map(o=>r.store.delete(o.id)),r.done])}catch(t){console.warn("Failed to evict old BLAST cache entries:",t)}}async function $t(){return(await(await X()).getAll(f)).toSorted((n,r)=>r.timestamp-n.timestamp)}async function Ot(e){await(await X()).delete(f,e)}var it="jbrowse-msaview-taxonomy-cache",T="common-names",at=2,Ce=$(it,at,e=>{e.objectStoreNames.contains(T)&&e.deleteObjectStore(T),e.createObjectStore(T,{keyPath:"taxid"})});function ct(e){return C("taxonomy cache read",async()=>{let n=(await Ce()).transaction(T,"readonly"),r=await Promise.all(e.map(o=>n.store.get(o)));return await n.done,r},[])}function Be(e){return C("taxonomy cache write",async()=>{let n=(await Ce()).transaction(T,"readwrite");for(let r of e)await n.store.put(r);await n.done},void 0)}async function vt(e,t,n){let r=[...new Set(e)],o=new Map,a=[],i=await ct(r);for(let u=0;u<r.length;u++){let d=r[u],h=i[u];h?o.set(d,{sciname:h.sciname,commonName:h.commonName}):a.push(d)}if(a.length===0)return o;let c=100,s=[];for(let u=0;u<a.length;u+=c){let d=a.slice(u,u+c),h=d.join(",");try{let l=await B(_({db:"taxonomy",id:h,retmode:"xml"}),{signal:t}),p=new Map,w=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,m;for(;(m=w.exec(l))!==null;){let b=Number(m[1]),g=m.index,D=1,x=g+m[0].length;for(;D>0&&x<l.length;){let O=l.indexOf("<Taxon>",x),j=l.indexOf("</Taxon>",x);if(j===-1)break;O!==-1&&O<j?(D++,x=O+7):(D--,x=j+8)}let N=l.slice(g,x),I=p.get(b),P=N.includes("<LineageEx>"),E=I?.includes("<LineageEx>");(!I||P&&!E)&&p.set(b,N)}for(let b of d){let g=p.get(b);if(g){let D=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),x=/<CommonName>(.*?)<\/CommonName>/.exec(g),N=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),I=D?.[1]??x?.[1],P=I&&k(I),E=k(N?.[1]??"");o.set(b,{sciname:E,commonName:P}),s.push({taxid:b,sciname:E,commonName:P})}}}catch(l){if(Z(l))throw await Be(s),l;console.error("Failed to fetch taxonomy data:",l),n?.(l)}}return s.length>0&&await Be(s),o}export{ut as a,Ee as b,ee as c,mt as d,dt as e,Ae as f,_e as g,lt as h,gt as i,ft as j,ht as k,Re as l,xt as m,$ as n,C as o,Rt as p,$t as q,Ot as r,L as s,_ as t,B as u,de as v,k as w,Le as x,ke as y,Bt as z,Ue as A,Ct as B,Tt as C,vt as D};
-//# sourceMappingURL=chunk-NI3VGKQP.js.map
+//# sourceMappingURL=chunk-BAM67QHH.js.map