jbrowse-plugin-msaview 3.9.0 → 4.0.0

package/dist/chunks/chunk-FCWXYIFC.js

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package/dist/chunks/chunk-IBBQUV2I.js

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package/dist/chunks/chunk-J6KYLXRD.js

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package/dist/chunks/chunk-MBI4TMKR.js

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+import{i as u,p,t as l}from"./chunk-PJZ3XTMG.js";function k(e,t){let n=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let s=t.get(e.taxid);s.commonName&&(n=s.commonName.split(" ").map(r=>r.charAt(0).toUpperCase()+r.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${n}`}function h(e){return e.replaceAll("-","")}var g="ncbiblast";function b(e){return(e.hits??[]).map(t=>{let n=Number.parseInt(t.hit_uni_ox??"",10);return{description:[{accession:t.hit_acc??"unknown",id:t.hit_id??t.hit_acc??"unknown",sciname:t.hit_uni_os??t.hit_os??"unknown",taxid:Number.isNaN(n)?void 0:n,title:t.hit_uni_de??t.hit_desc}],hsps:(t.hit_hsps??[]).flatMap(s=>s.hsp_hseq?[{hseq:s.hsp_hseq}]:[])}})}function R(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${g}/summary?jobId=${e}`}async function w({query:e,blastDatabase:t,maxHits:n,onProgress:s,onRid:r,signal:i}){let o=n?String(p(n)):void 0,a=await u({tool:g,label:"BLAST",params:{program:"blastp",stype:"protein",database:t,sequence:e,...o?{alignments:o,scores:o}:{}},onProgress:s,onRid:r,signal:i}),c=b(JSON.parse(await a.result("json")));if(c.length===0)throw new Error("No hits found");return{rid:a.jobId,hits:c}}var j=async({database:e,...t})=>{let{hits:n,rid:s}=await w({blastDatabase:e,...t});return{rid:s,hits:n.map(r=>({...r.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},sequence:h(r.hsps[0]?.hseq??"")}))}};var d="hmmer3_phmmer";function O(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${d}/summary?jobId=${e}`}function H(e){return e.startsWith(`${d}-`)}function x({rf:e,query:t}){let n=0,s=Array.from(e,r=>r==="x"?t[n++]??"-":"-").join("");if(n!==t.length)throw new Error(`phmmer alignment has ${n} match columns for a query of ${t.length} residues, so the query row cannot be placed`);return s}function _(e){let t=(e??"").replace("[subseq from] ","");if(t.includes("^|^")){let r=t.split("^|^"),i=r[6];return{id:r[0]||void 0,sciname:r[5]||"unknown",taxid:i&&/^\d+$/.test(i)?Number.parseInt(i,10):void 0,title:r[2]||void 0}}let n=/OS=(.*?)\s+(?:OX|GN|PE|SV)=/.exec(t)?.[1],s=/OX=(\d+)/.exec(t)?.[1];return{id:void 0,sciname:n??"unknown",taxid:s?Number.parseInt(s,10):void 0,title:t.split(" OS=")[0]||void 0}}function y(e){let t=e.lastIndexOf("/"),n=t===-1?void 0:/^\d+-\d+$/.exec(e.slice(t+1))?.[0],s=n===void 0?e:e.slice(0,t),r=s.split("|");return r.length===3?{accession:r[1],id:r[2],range:n}:{accession:s,id:s,range:n}}function S({stockholm:e,query:t}){let{gc:n,gs:s,seqdata:r,seqname:i}=new l(e,0).getMSA(),o=n.RF;if(!o)throw new Error("phmmer alignment has no #=GC RF line");return{queryRow:x({rf:o,query:t}),rows:i.map(a=>{let{id:c,...f}=_(s.DE?.[a]?.[0]),m=y(a);return{...m,id:m.id===m.accession&&c?c:m.id,...f,aligned:(r[a]??"").replaceAll(".","-").toUpperCase()}})}}async function q({query:e,database:t,maxHits:n,onProgress:s,onRid:r,signal:i}){let o=await u({tool:d,label:"phmmer",params:{database:t,sequence:e,alignView:"true",...n?{nhits:String(n)}:{}},onProgress:s,onRid:r,signal:i}),a=S({stockholm:await o.result("sto"),query:e});if(a.rows.length===0)throw new Error("No hits found");return{rid:o.jobId,...a}}function B(e){return e.map(({aligned:t,...n})=>({...n,sequence:t}))}var J=async({database:e,...t})=>{let{rows:n,queryRow:s,rid:r}=await q({database:e,...t});return{rid:r,queryRow:s,hits:B(n)}};export{k as a,R as b,j as c,O as d,H as e,J as f};
+//# sourceMappingURL=chunk-MBI4TMKR.js.map

package/dist/chunks/chunk-MBI4TMKR.js.map

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+{
+  "version": 3,
+  "sources": ["../../src/LaunchMsaView/components/util.ts", "../../src/utils/ebiBlast.ts", "../../src/utils/phmmer.ts"],
+  "sourcesContent": ["import type { TaxonomyInfo } from '../../utils/taxonomyNames'\n\nexport function makeId(\n  h: { accession: string; sciname: string; taxid?: number },\n  taxonomyInfo?: Map<number, TaxonomyInfo>,\n) {\n  let speciesName = h.sciname.replaceAll(' ', '_')\n  if (h.taxid && taxonomyInfo?.has(h.taxid)) {\n    const info = taxonomyInfo.get(h.taxid)!\n    if (info.commonName) {\n      speciesName = info.commonName\n        .split(' ')\n        .map(word => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase())\n        .join('_')\n    }\n  }\n  return `${h.accession}-${speciesName}`\n}\n\nexport function strip(s: string) {\n  return s.replaceAll('-', '')\n}\n", "import { snapBlastHitCount } from '../LaunchMsaView/components/BlastQuery/consts'\nimport { strip } from '../LaunchMsaView/components/util'\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { BlastDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend } from './homologSearch'\nimport type { BlastHit } from './types'\n\nconst TOOL = 'ncbiblast'\n\n/**\n * The subset of EBI's ncbiblast JSON result this plugin reads. The service\n * returns a great deal more per hit (urls, bit scores, e-values, the match\n * string); only what the MSA rows are built from is typed here.\n */\ninterface EbiBlastJson {\n  hits?: {\n    hit_acc?: string\n    hit_id?: string\n    hit_desc?: string\n    /** the UniProt fields are absent on hits from non-UniProt databases */\n    hit_os?: string\n    hit_uni_de?: string\n    hit_uni_os?: string\n    /** NCBI taxon id, delivered as a string */\n    hit_uni_ox?: string\n    hit_hsps?: { hsp_hseq?: string }[]\n  }[]\n}\n\n/**\n * Map EBI's hit shape onto the normalized one. Exported for testing against a\n * captured response \u2014 the field names are the whole risk here, and nothing else\n * in CI would notice if EBI renamed one.\n */\nexport function normalizeEbiBlastHits(result: EbiBlastJson): BlastHit[] {\n  return (result.hits ?? []).map(hit => {\n    const taxid = Number.parseInt(hit.hit_uni_ox ?? '', 10)\n    return {\n      description: [\n        {\n          accession: hit.hit_acc ?? 'unknown',\n          id: hit.hit_id ?? hit.hit_acc ?? 'unknown',\n          sciname: hit.hit_uni_os ?? hit.hit_os ?? 'unknown',\n          taxid: Number.isNaN(taxid) ? undefined : taxid,\n          // hit_uni_de is the bare protein name; hit_desc repeats it with the\n          // OS=/OX=/GN= suffix that makeId already covers with real columns\n          title: hit.hit_uni_de ?? hit.hit_desc,\n        },\n      ],\n      hsps: (hit.hit_hsps ?? []).flatMap(hsp =>\n        hsp.hsp_hseq ? [{ hseq: hsp.hsp_hseq }] : [],\n      ),\n    }\n  })\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error \u2014 so it has to\n * be EBI's own results UI, not the REST result endpoint, which does not exist\n * yet at the moment the link is on screen.\n */\nexport function ebiBlastResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\nexport async function queryEbiBlast({\n  query,\n  blastDatabase,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  blastDatabase: BlastDatabase\n  /** rounded up to a count EBI accepts; their default of 50 when omitted */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const hitCount = maxHits ? String(snapBlastHitCount(maxHits)) : undefined\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'BLAST',\n    params: {\n      program: 'blastp',\n      stype: 'protein',\n      database: blastDatabase,\n      sequence: query,\n      ...(hitCount ? { alignments: hitCount, scores: hitCount } : {}),\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  const hits = normalizeEbiBlastHits(\n    JSON.parse(await job.result('json')) as EbiBlastJson,\n  )\n  if (hits.length === 0) {\n    throw new Error('No hits found')\n  }\n  return { rid: job.jobId, hits }\n}\n\n/**\n * BLAST as a search backend. Its alignments are pairwise and one hit at a\n * time, so they are stripped back off and the hits go to an aligner as bare\n * sequences: no `queryRow`.\n */\nexport const searchEbiBlast: SearchBackend = async ({\n  database,\n  ...request\n}) => {\n  const { hits, rid } = await queryEbiBlast({\n    blastDatabase: database as BlastDatabase,\n    ...request,\n  })\n  return {\n    rid,\n    hits: hits.map(hit => ({\n      ...(hit.description[0] ?? {\n        accession: 'unknown',\n        id: 'unknown',\n        sciname: 'unknown',\n      }),\n      sequence: strip(hit.hsps[0]?.hseq ?? ''),\n    })),\n  }\n}\n", "import { StockholmMSA } from 'msa-parsers'\n\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend, SearchHit } from './homologSearch'\n\nconst TOOL = 'hmmer3_phmmer'\n\nexport interface PhmmerRow {\n  accession: string\n  id: string\n  sciname: string\n  taxid?: number\n  title?: string\n  /** the matched envelope on the target, e.g. '503-912', absent if unparseable */\n  range?: string\n  /** the row as phmmer aligned it, uppercased with '.' inserts turned into '-' */\n  aligned: string\n}\n\nexport interface PhmmerAlignment {\n  rows: PhmmerRow[]\n  /**\n   * the query, placed into the same columns. phmmer does not put the query in\n   * its own output, so this is derived \u2014 see buildQueryRow.\n   */\n  queryRow: string\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error.\n *\n * The category has to be sss: jdispatcher serves its shell with a 200 for any\n * category, so /pfa/ and /psa/ look fine to a fetch and render \"Page Not Found\"\n * in a browser.\n */\nexport function phmmerResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\n/** EBI job ids are prefixed with the tool that made them */\nexport function isPhmmerJobId(jobId: string) {\n  return jobId.startsWith(`${TOOL}-`)\n}\n\n/**\n * phmmer aligns every hit to a profile built from the query, one match state\n * per query residue, and marks those columns 'x' in #=GC RF. So the query's own\n * row is exactly recoverable: walk RF, consume a query residue at each match\n * column, gap everywhere else.\n *\n * This is the one piece of real logic here rather than a library call, and it\n * is checked hard: if the match columns do not account for the query exactly,\n * the columns and the query have drifted apart, and a query row that is off by\n * even one residue would silently mis-map every column to the genome. Throwing\n * is much better than drawing that.\n */\nfunction buildQueryRow({ rf, query }: { rf: string; query: string }) {\n  let consumed = 0\n  const row = Array.from(rf, c =>\n    c === 'x' ? (query[consumed++] ?? '-') : '-',\n  ).join('')\n  if (consumed !== query.length) {\n    throw new Error(\n      `phmmer alignment has ${consumed} match columns for a query of ${query.length} residues, so the query row cannot be placed`,\n    )\n  }\n  return row\n}\n\n/**\n * '[subseq from] Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2' is what a\n * UniProt target's #=GS DE looks like. The representative-proteome databases\n * (rp15..rp75) write the same facts as caret-pipe fields instead --\n * 'P53_HUMAN^|^DNHU53^|^Cellular tumor antigen p53^|^...^|^Homo sapiens^|^9606^|^Euk/mammal^|^40674'\n * -- so both grammars are read. Hits from the non-UniProt databases phmmer\n * also offers (PDB, AlphaFold, MEROPS...) carry neither, so every field here\n * is optional.\n */\nfunction parseDescription(de: string | undefined) {\n  const text = (de ?? '').replace('[subseq from] ', '')\n  if (text.includes('^|^')) {\n    const fields = text.split('^|^')\n    const ox = fields[6]\n    return {\n      id: fields[0] || undefined,\n      sciname: fields[5] || 'unknown',\n      taxid: ox && /^\\d+$/.test(ox) ? Number.parseInt(ox, 10) : undefined,\n      title: fields[2] || undefined,\n    }\n  }\n  const sciname = /OS=(.*?)\\s+(?:OX|GN|PE|SV)=/.exec(text)?.[1]\n  const ox = /OX=(\\d+)/.exec(text)?.[1]\n  return {\n    id: undefined,\n    sciname: sciname ?? 'unknown',\n    taxid: ox ? Number.parseInt(ox, 10) : undefined,\n    title: text.split(' OS=')[0] || undefined,\n  }\n}\n\n/**\n * Target names look like 'sp|P02768|ALBU_HUMAN/1-609' for UniProt databases and\n * like anything at all for the others, so an unrecognized name becomes its own\n * accession rather than being dropped.\n */\nfunction parseName(name: string) {\n  const slash = name.lastIndexOf('/')\n  const range =\n    slash === -1 ? undefined : /^\\d+-\\d+$/.exec(name.slice(slash + 1))?.[0]\n  const bare = range === undefined ? name : name.slice(0, slash)\n  const parts = bare.split('|')\n  return parts.length === 3\n    ? { accession: parts[1]!, id: parts[2]!, range }\n    : { accession: bare, id: bare, range }\n}\n\n/**\n * Exported for testing against a captured .sto \u2014 the annotation names (RF, the\n * DE line's OS=/OX=) are the whole risk in this mapping, and nothing else in CI\n * would notice if HMMER or EBI changed one.\n */\nexport function parsePhmmerAlignment({\n  stockholm,\n  query,\n}: {\n  stockholm: string\n  query: string\n}): PhmmerAlignment {\n  const { gc, gs, seqdata, seqname } = new StockholmMSA(stockholm, 0).getMSA()\n  const rf = gc.RF\n  if (!rf) {\n    throw new Error('phmmer alignment has no #=GC RF line')\n  }\n\n  return {\n    queryRow: buildQueryRow({ rf, query }),\n    rows: seqname.map(name => {\n      const { id, ...description } = parseDescription(gs.DE?.[name]?.[0])\n      const parsed = parseName(name)\n      return {\n        ...parsed,\n        // the rp databases name a row by bare accession and put the mnemonic\n        // id in the description instead\n        id: parsed.id === parsed.accession && id ? id : parsed.id,\n        ...description,\n        // insert columns come back lowercase with '.' for gaps; the MSA renderer\n        // looks colors up by the literal letter, so lowercase would draw\n        // uncolored. The insert columns stay visible as gaps in the query row.\n        aligned: (seqdata[name] ?? '').replaceAll('.', '-').toUpperCase(),\n      }\n    }),\n  }\n}\n\nexport async function queryPhmmer({\n  query,\n  database,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  database: PhmmerDatabase\n  /** EBI's `nhits`, 100 when omitted */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'phmmer',\n    params: {\n      database,\n      sequence: query,\n      // the alignment is the whole point of using phmmer here\n      alignView: 'true',\n      ...(maxHits ? { nhits: String(maxHits) } : {}),\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  const alignment = parsePhmmerAlignment({\n    stockholm: await job.result('sto'),\n    query,\n  })\n  if (alignment.rows.length === 0) {\n    throw new Error('No hits found')\n  }\n  return { rid: job.jobId, ...alignment }\n}\n\n/** phmmer's rows as search hits: the aligned row is the hit's sequence. */\nexport function toSearchHits(rows: PhmmerRow[]): SearchHit[] {\n  return rows.map(({ aligned, ...rest }) => ({ ...rest, sequence: aligned }))\n}\n\n/**\n * phmmer as a search backend. It aligns every hit to a profile of the query as\n * it searches, so the result carries `queryRow` and no aligner runs after it.\n */\nexport const searchEbiPhmmer: SearchBackend = async ({\n  database,\n  ...request\n}) => {\n  const { rows, queryRow, rid } = await queryPhmmer({\n    database: database as PhmmerDatabase,\n    ...request,\n  })\n  return { rid, queryRow, hits: toSearchHits(rows) }\n}\n"],
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+`);for(let i of a){let c;if(j.test(i))s&&r.push(s),s=B(),o=!1;else if(it.test(i))s&&r.push(s),s=null;else if(c=at.exec(i)){s=b(s,!!n.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=ct.exec(i))s=b(s,!!n.strict),s.gc[c[1]]=(s.gc[c[1]]??"")+c[2];else if(c=ut.exec(i)){s=b(s,!!n.strict);let u=s.gs[c[2]]??=Object.create(null);(u[c[1]]??=[]).push(c[3])}else if(c=pt.exec(i)){s=b(s,!!n.strict);let u=s.gr[c[2]]??=Object.create(null);u[c[1]]=(u[c[1]]??"")+c[3]}else if(c=ft.exec(i)){s=b(s,!!n.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(lt.test(i)&&n.strict)throw new Error("Malformed line")}return s&&r.push(s),r}var m=class extends p{data;MSA;constructor(t,n){let r=U(t),s=r[n]??r[0];if(!s)throw new Error("No alignments found in Stockholm file");super(s.seqname.map(o=>[o,s.seqdata[o]??""])),this.data=r,this.MSA=s}getMSA(){return this.MSA}get alignmentNames(){return this.data.map((t,n)=>t.gf.DE?.[0]??`Alignment ${n+1}`)}getHeader(){let t=this.MSA.gs.AC??{},n=this.MSA.gs.DR??{};return{General:this.MSA.gf,Accessions:Object.fromEntries(Object.entries(t).map(([r,s])=>[r,s[0]])),Dbxref:Object.fromEntries(Object.entries(n).map(([r,s])=>[r,s.join("; ")]))}}getRowData(t){return{name:t,accession:this.MSA.gs.AC?.[t]?.[0],dbxref:this.MSA.gs.DR?.[t]?.join("; ")}}getStructures(){let t=/PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/,n=this.MSA.gs.DR??{},r={};for(let[s,o]of Object.entries(n))for(let a of o){let i=t.exec(a);i&&(r[s]??=[]).push({pdb:i[1].toLowerCase(),chain:i[2],startPos:+i[3],endPos:+i[4]})}return r}getTree(){let t=this.MSA.gf.NH?.[0];return t?M(S(t)):super.getTree()}get seqConsensus(){return this.MSA.gc.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc.SS_cons}get tracks(){let{seq_cons:t,SS_cons:n,...r}=this.MSA.gc;return[{id:"seqConsensus",name:"Sequence consensus",data:t,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:n,customColorScheme:v},...Object.entries(r).map(([s,o])=>({id:`gc-${s}`,name:s,data:o,customColorScheme:G(s)})),...Object.entries(this.MSA.gr).flatMap(([s,o])=>Object.entries(o).map(([a,i])=>({id:`gr-${a}-${s}`,name:`${a} ${s}`,data:i,customColorScheme:G(s),defaultOff:!0})))]}},v={"<":"lightblue","(":"lightblue","[":"lightblue","{":"lightblue",">":"pink",")":"pink","]":"pink","}":"pink"};function G(e){return e==="SS"||e.endsWith("_SS")?v:{}}function E(e){return/^(#.*\n)*>/.test(e)}function C(e){let t=[],n=new Set,r,s=()=>{r&&!n.has(r.id)&&(n.add(r.id),t.push({id:r.id,seq:r.lines.join("").replaceAll(/\s/g,"")}))},o=0;for(let a of e.split(`
+`))a.startsWith(">")?(s(),o++,r={id:/^>\s*(\S*)/.exec(a)[1]||`unnamed_${o}`,lines:[]}):r?.lines.push(a);return s(),t}function A(e){return typeof e=="string"?C(e):e}var mt=65,dt=90,ht=97,gt=122,St=45;function H(e){return e>=ht&&e<=gt}function K(e){return e>=mt&&e<=dt||e===St}function bt(e){let t=[],n=[""];for(let r of e){let s=r.charCodeAt(0);K(s)?(t.push(r),n.push("")):H(s)&&(n[n.length-1]+=r.toUpperCase())}return{matches:t,inserts:n}}var l=class extends p{constructor(t){let n=A(t),r=xt(n.map(s=>s.seq));super(n.map((s,o)=>[s.id,r[o]]))}static sniff(t){if(typeof t=="string"&&!E(t))return!1;let n=A(t).map(o=>o.seq).filter(o=>!!o);if(n.length<2||new Set(n.map(o=>o.length)).size===1)return!1;let r=!1,s;for(let o of n){let a=0;for(let i=0;i<o.length;i++){let c=o.charCodeAt(i);K(c)?a++:H(c)&&(r=!0)}if(s!==void 0&&a!==s)return!1;s=a}return r}};function xt(e){let t=e.map(bt),n=0;for(let{matches:s}of t)n=Math.max(n,s.length);let r=new Array(n+1).fill(0);for(let{inserts:s}of t)for(let[o,a]of s.entries())r[o]=Math.max(r[o],a.length);return t.map(({matches:s,inserts:o})=>{let a=[];for(let i=0;i<=n;i++){let c=o[i]??"";a.push(c,".".repeat(r[i]-c.length)),i<n&&a.push(s[i]??"-")}return a.join("")})}var d=class extends p{MSA;constructor(t){let n=F(t);super(n.alns.map(r=>[r.id,r.seq])),this.MSA=n}getHeader(){return this.MSA.header}get seqConsensus(){return this.MSA.consensus}};var h=class extends p{constructor(t){super(O(t).map(n=>[n.protein,n.seq]))}};var g=class extends p{colonNormalized=new Map;constructor(t){let n=A(t);super(n.map(r=>[r.id,r.seq]));for(let{id:r}of n)r.includes(":")&&this.colonNormalized.set(r.replaceAll(":","_"),r)}getRow(t){return this.rows.get(t)??this.rows.get(this.colonNormalized.get(t)??"")??""}};var wt=/^<(!doctype\s+html|html[\s>])/i,Et=/^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i;function Rt(e,t=0,n){let r=e.replace(/^\uFEFF/,"").replaceAll(/\r\n?/g,`
+`).trimStart();if(wt.test(r))throw new Error("Received an HTML page, not an alignment. Check that the URL points at the file itself");if(n==="stockholm")return new m(r,t);if(n==="a3m")return new l(r);if(n==="fasta")return new g(r);if(n==="emf")return new h(r);if(n==="clustal")return new d(r);if(x(r))return new m(r,t);if(E(r)){let o=C(r);return l.sniff(o)?new l(o):new g(o)}if(r.startsWith("SEQ"))return new h(r);if(Et.test(r))return new d(r);let s=r.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 Tt(e){return e.replaceAll(/[.-]/g,"")}export{P as a,w as b,kt as c,N as d,k as e,Pt as f,V as g,q as h,Ut as i,vt 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,m as t,Rt as u,Tt as v};
+//# sourceMappingURL=chunk-PJZ3XTMG.js.map

package/dist/chunks/chunk-PJZ3XTMG.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/useLocalStorage.ts", "../../src/utils/fetch.ts", "../../src/utils/poll.ts", "../../src/utils/ebiJobDispatcher.ts", "../../src/LaunchMsaView/components/BlastQuery/consts.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/util.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/BaseMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/parseNewick.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/stockholmParser.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/StockholmMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/fastaRecords.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/A3mMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/ClustalMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/EmfMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/FastaMSA.ts", "../../node_modules/.pnpm/msa-parsers@8.3.0/node_modules/msa-parsers/src/msa/index.ts"],
+  "sourcesContent": ["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", "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 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 Error(\n      `HTTP ${response.status} fetching ${url} ${await response.text()}`,\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 { 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. A deployment that sends real volume should point this\n * at its own maintainer via the BLAST settings dialog \u2014 otherwise every\n * msaview job in the world is attributed to one person.\n */\nexport const EBI_EMAIL_STORAGE_KEY = 'msa-ebiContactEmail'\nexport const DEFAULT_EBI_EMAIL = 'colin.diesh@gmail.com'\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": 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package/dist/chunks/chunk-QAC6JSDZ.js

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+function k(t){let e=t.split(`
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+`).map(n=>n.trim()).filter(n=>!!n),r=[],s="";for(let n of e)if(n.startsWith("SEQ"))r.push(n);else{if(n.startsWith("DATA"))continue;if(n.startsWith("//"))break;s=n}let o=r.map(n=>{let[,i,c,p,a,u,l,f,h]=n.split(" ");return{species:i,protein:c,chr:p,start:+a,end:+u,strand:+l,geneId:f,unknown:h}});return{tree:s,seqs:o}}function q(t){let e=/\(?(\d+(\.\d+)+)\)?/.exec(t);return e&&e.length>1?e[1]:""}function m(t){let e=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];e.some(s=>t.startsWith(s))||console.warn(`${t} is not a known CLUSTAL header: ${e.join(",")}, proceeding but could indicate an issue`);let r=q(t);return{info:t,version:r}}function d(t){let e=t.next();for(;!e.done&&e.value.trim()==="";)e=t.next();return e.value}function x(t){let e=t.split(/\s+/),r=t.slice(e[0].length),s=e[0].length+r.indexOf(e[1]),o=s+e[1].length;return[s,o]}function g(t){let e=d(t),r=[],s="";if(!e)return;for(;e;)e.startsWith(" ")?s=e:r.push(e),e=t.next().value;let[o,n]=x(r[0]),c=r.map(l=>l.split(/\s+/)).map(l=>l[0]),p=r.map(l=>l.slice(o,n)),a=s.slice(o,n),u=p[0].length-a.length;return u&&(a+=" ".repeat(u)),{ids:c,seqs:p,consensus:a}}function w(t){let e,r=g(t);if(r!==void 0)for(;e=g(t);){for(let s=0;s<e.seqs.length;s++)r.seqs[s]+=e.seqs[s];r.consensus+=e.consensus}return r}function E(t){let e=d(t);if(!e)throw new Error("Empty file received");let r=m(e),s=w(t);if(s===void 0)throw new Error("No blocks parsed");let o=s.seqs.map((i,c)=>({id:s.ids[c],seq:i})),{consensus:n}=s;if(n.length!==o[0].seq.length)throw new Error(`Consensus length != sequence length. Con ${n.length} seq ${o[0].seq.length}`);return{consensus:n,alns:o,header:r}}function W(t){let e=t.split(`
+`)[Symbol.iterator]();return E(e)}export{W as a,k as b,S as c};
+//# sourceMappingURL=chunk-QAC6JSDZ.js.map

package/dist/chunks/chunk-QAC6JSDZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/emf-js@2.0.0/node_modules/emf-js/src/index.ts", "../../node_modules/.pnpm/clustal-js@2.0.18/node_modules/clustal-js/src/util.ts", "../../node_modules/.pnpm/clustal-js@2.0.18/node_modules/clustal-js/src/index.ts"],
+  "sourcesContent": ["export interface Row {\n  id: string\n  seq: string\n}\n\nexport function parseEmfAln(contents: string) {\n  const lines = contents\n    .split('\\n')\n    .map(f => f.trim())\n    .filter(f => !!f)\n  const seqs = []\n  const alns = []\n  for (const line of lines) {\n    if (line.startsWith('SEQ')) {\n      seqs.push(line)\n    } else if (line.startsWith('DATA')) {\n      continue\n    } else if (line.startsWith('//')) {\n      break\n    } else {\n      alns.push(line)\n    }\n  }\n  const arr = seqs.map(s => {\n    const [, species, protein, chr, start, end, strand, geneId, unknown] =\n      s.split(' ')\n    return {\n      species,\n      protein,\n      chr,\n      start: +start,\n      end: +end,\n      strand: +strand,\n      geneId,\n      unknown,\n      seq: '',\n    }\n  })\n  for (const aln of alns) {\n    for (let j = 0; j < seqs.length; j++) {\n      arr[j].seq += aln[j]\n    }\n  }\n  return arr\n}\n\nexport function parseEmfTree(contents: string) {\n  const lines = contents\n    .split('\\n')\n    .map(f => f.trim())\n    .filter(f => !!f)\n  const seqs = []\n  let tree = ''\n  for (const line of lines) {\n    if (line.startsWith('SEQ')) {\n      seqs.push(line)\n    } else if (line.startsWith('DATA')) {\n      continue\n    } else if (line.startsWith('//')) {\n      break\n    } else {\n      tree = line\n    }\n  }\n  const arr = seqs.map(s => {\n    const [, species, protein, chr, start, end, strand, geneId, unknown] =\n      s.split(' ')\n    return {\n      species,\n      protein,\n      chr,\n      start: +start,\n      end: +end,\n      strand: +strand,\n      geneId,\n      unknown,\n    }\n  })\n\n  return { tree, seqs: arr }\n}\n", "export function parseVersion(line: string) {\n  const res = /\\(?(\\d+(\\.\\d+)+)\\)?/.exec(line)\n  return res && res.length > 1 ? res[1] : ''\n}\nexport function parseHeader(info: string) {\n  const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign']\n\n  if (!knownHeaders.some(l => info.startsWith(l))) {\n    console.warn(\n      `${info} is not a known CLUSTAL header: ${knownHeaders.join(\n        ',',\n      )}, proceeding but could indicate an issue`,\n    )\n  }\n  const version = parseVersion(info)\n  return { info, version }\n}\n\nexport function getFirstNonEmptyLine(arr: Iterator<string>): string {\n  // There should be two blank lines after the header line\n  let line = arr.next()\n  while (!line.done && line.value.trim() === '') {\n    line = arr.next()\n  }\n  return line.value!\n}\n\nexport function getSeqBounds(line: string) {\n  const fields = line.split(/\\s+/)\n  const temp = line.slice(fields[0]!.length)\n  const s = fields[0]!.length + temp.indexOf(fields[1]!)\n  const e = s + fields[1]!.length\n  return [s, e] as const\n}\n\n// Use the first block to get the sequence identifiers\nexport function parseBlock(arr: Iterator<string>) {\n  let line = getFirstNonEmptyLine(arr)\n  const block = []\n  let consensusLine = ''\n  if (!line) {\n    return undefined\n  }\n\n  while (line) {\n    if (line.startsWith(' ')) {\n      consensusLine = line\n    } else {\n      block.push(line)\n    }\n    line = arr.next().value\n  }\n  const [start, end] = getSeqBounds(block[0]!)\n  const fields = block.map(s => s.split(/\\s+/))\n  const ids = fields.map(s => s[0]!)\n  const seqs = block.map(s => s.slice(start, end))\n  let consensus = consensusLine.slice(start, end)\n\n  // handle if the consensus trailing whitespace got trimmed\n  const remainder = seqs[0]!.length - consensus.length\n  if (remainder) {\n    consensus += ' '.repeat(remainder)\n  }\n  return {\n    ids,\n    seqs,\n    consensus,\n  }\n}\n\nexport function parseBlocks(arr: Iterator<string>) {\n  let block\n  const res = parseBlock(arr)\n  if (res !== undefined) {\n    while ((block = parseBlock(arr))) {\n      for (let i = 0; i < block.seqs.length; i++) {\n        res.seqs[i] += block.seqs[i]!\n      }\n      res.consensus += block.consensus\n    }\n  }\n  return res\n}\n", "import { parsePairwiseBlocks } from './pairwise.ts'\nimport { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util.ts'\n\nexport function parseClustalIter(arr: Iterator<string>) {\n  const line = getFirstNonEmptyLine(arr)\n  if (!line) {\n    throw new Error('Empty file received')\n  }\n  const header = parseHeader(line)\n\n  const res = parseBlocks(arr)\n  if (res === undefined) {\n    throw new Error('No blocks parsed')\n  }\n\n  const alns = res.seqs.map((n, index) => ({ id: res.ids[index]!, seq: n }))\n  const { consensus } = res\n  if (consensus.length !== alns[0]!.seq.length) {\n    throw new Error(\n      `Consensus length != sequence length. Con ${consensus.length} seq ${alns[0]!.seq.length}`,\n    )\n  }\n\n  return { consensus, alns, header }\n}\n\nexport interface Row {\n  id: string\n  seq: string\n}\n\nexport function parse(contents: string) {\n  const iter = contents.split('\\n')[Symbol.iterator]()\n  return parseClustalIter(iter)\n}\n\nexport function parsePairwise(contents: string) {\n  const filtered = contents\n    .split('\\n')\n    .filter(f => !f.startsWith('#'))\n    .join('\\n')\n\n  const res = parsePairwiseBlocks(filtered.split('\\n')[Symbol.iterator]())\n  if (res === undefined) {\n    throw new Error('No blocks parsed')\n  }\n\n  const alns = res.seqs.map((n, index) => ({ id: res.ids[index]!, seq: n }))\n  const { consensus } = res\n  const firstAln = alns[0]\n  if (!firstAln) {\n    throw new Error('No alignments found')\n  }\n  if (consensus.length !== firstAln.seq.length) {\n    throw new Error(\n      `Consensus length !== sequence length. Con ${consensus.length} seq ${firstAln.seq.length}`,\n    )\n  }\n  if (alns.length !== 2) {\n    throw new Error(\n      `Expected exactly 2 sequences in pairwise alignment, got ${alns.length}`,\n    )\n  }\n  return {\n    consensus,\n    alns: alns as [Row, Row],\n  }\n}\n"],
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+  "names": ["parseEmfAln", "contents", "lines", "f", "seqs", "alns", "line", "arr", "s", "species", "protein", "chr", "start", "end", "strand", "geneId", "unknown", "aln", "j", "parseEmfTree", "tree", "parseVersion", "line", "res", "parseHeader", "info", "knownHeaders", "l", "version", "getFirstNonEmptyLine", "arr", "getSeqBounds", "fields", "temp", "e", "parseBlock", "block", "consensusLine", "start", "end", "ids", "s", "seqs", "consensus", "remainder", "parseBlocks", "i", "parseClustalIter", "arr", "line", "getFirstNonEmptyLine", "header", "parseHeader", "res", "parseBlocks", "alns", "n", "index", "consensus", "parse", "contents", "iter"]
+}