jbrowse-plugin-msaview 5.2.0 → 5.3.0

package/dist/chunks/chunk-DEFUNIWW.js

@@ -0,0 +1,8 @@
+import{a as E,b as O}from"./chunk-K55ZVN73.js";import{a as q}from"./chunk-73KAPCJ2.js";function C(r){return Object.fromEntries(r.map(e=>[e.xref[0]?.id,e]).filter(e=>e[0]!==void 0))}function F(r){return Object.entries(r).flatMap(([e,{matches:n}])=>n.flatMap(({signature:t,locations:s})=>{let{entry:o}=t,c=o?.accession??t.accession;if(!c)return[];let i=o?.name??t.name??c;return s.map(({start:a,end:f,strand:u})=>({id:e,accession:c,name:i,description:o?.description??t.description??i,start:a,end:f,strand:u}))}))}function N(r){return F(C(r.results))}function S(r,e=[]){return["##gff-version 3",...e.map(n=>`# ${n}`),...r.map(n=>{let{accession:t,name:s,description:o,featureType:c}=n,{id:i,start:a,end:f,strand:u}=n;return[i.replaceAll(/[%\t\n\r]/g,encodeURIComponent),"InterProScan",c??"protein_match",a,f,".",u===void 0?".":u>0?"+":"-",".",[`Name=${encodeURIComponent(t)}`,`signature_desc=${encodeURIComponent(s)}`,`description=${encodeURIComponent(o)}`].join(";")].join("	")})].join(`
+`)}function B(r){let e=r.trimStart();if(!e.startsWith("{"))return r;let n=JSON.parse(e);return S(N(n))}function T(r,e="node",n=0){let t=(c,i)=>({...c,id:i,name:c.name||i,children:[]}),s=t(r,`${e}-${n}`),o=[{src:r,out:s,depth:n}];for(;o.length>0;){let{src:c,out:i,depth:a}=o.pop();if(c.children){i.children=c.children.map((f,u)=>t(f,`${i.id}-${u}-${a+1}`));for(let[f,u]of c.children.entries())o.push({src:u,out:i.children[f],depth:a+1})}}return s}var l=class{rows=new Map;names;width;constructor(e){for(let[n,t]of e)this.rows.has(n)||this.rows.set(n,t);this.names=[...this.rows.keys()]}getRow(e){return this.rows.get(e)??""}getNames(){return this.names}getWidth(){return this.width??=this.getNames().reduce((e,n)=>Math.max(e,this.getRow(n).length),0),this.width}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(e=>({id:e,children:[],name:e}))}}getRowData(e){}getStructures(){return{}}getHeader(){return{}}get alignmentNames(){return[]}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}};function R(r){return/^(#.*\n)*>/.test(r)}function b(r){let e=[],n=new Set,t,s=()=>{t&&!n.has(t.id)&&(n.add(t.id),e.push({id:t.id,seq:t.lines.join("").replaceAll(/\s/g,"")}))},o=0;for(let c of r.split(`
+`))c.startsWith(">")?(s(),o++,t={id:/^>\s*(\S*)/.exec(c)[1]||`unnamed_${o}`,lines:[]}):t?.lines.push(c);return s(),e}function x(r){return typeof r=="string"?b(r):r}var W=65,z=90,v=97,K=122,X=45;function _(r){return r>=v&&r<=K}function $(r){return r>=W&&r<=z||r===X}function Q(r){let e=[],n=[""];for(let t of r){let s=t.charCodeAt(0);$(s)?(e.push(t),n.push("")):_(s)&&(n[n.length-1]+=t.toUpperCase())}return{matches:e,inserts:n}}var p=class extends l{constructor(e){let n=x(e),t=Y(n.map(s=>s.seq));super(n.map((s,o)=>[s.id,t[o]]))}static sniff(e){if(typeof e=="string"&&!R(e))return!1;let n=x(e).map(o=>o.seq).filter(o=>!!o);if(n.length<2||new Set(n.map(o=>o.length)).size===1)return!1;let t=!1,s;for(let o of n){let c=0;for(let i=0;i<o.length;i++){let a=o.charCodeAt(i);$(a)?c++:_(a)&&(t=!0)}if(s!==void 0&&c!==s)return!1;s=c}return t}};function Y(r){let e=r.map(Q),n=0;for(let{matches:s}of e)n=Math.max(n,s.length);let t=new Array(n+1).fill(0);for(let{inserts:s}of e)for(let[o,c]of s.entries())t[o]=Math.max(t[o],c.length);return e.map(({matches:s,inserts:o})=>{let c=[];for(let i=0;i<=n;i++){let a=o[i]??"";c.push(a,".".repeat(t[i]-a.length)),i<n&&c.push(s[i]??"-")}return c.join("")})}var m=class extends l{MSA;constructor(e){let n=E(e);super(n.alns.map(t=>[t.id,t.seq])),this.MSA=n}getHeader(){return this.MSA.header}get seqConsensus(){return this.MSA.consensus}};var d=class extends l{constructor(e){super(O(e).map(n=>[n.protein,n.seq]))}};var h=class extends l{colonNormalized=new Map;constructor(e){let n=x(e);super(n.map(t=>[t.id,t.seq]));for(let{id:t}of n)t.includes(":")&&this.colonNormalized.set(t.replaceAll(":","_"),t)}getRow(e){return this.rows.get(e)??this.rows.get(this.colonNormalized.get(e)??"")??""}};function A(r){return q(r,{postParenNumeric:"name"})}function y(){return{gf:Object.create(null),gc:Object.create(null),gs:Object.create(null),gr:Object.create(null),seqname:[],seqdata:Object.create(null)}}function w(r,e){if(r)return r;if(e)throw new Error("No format header: # STOCKHOLM 1.0");return y()}var j=/^# STOCKHOLM 1.0/,J=/^\/\/\s*$/,V=/^#=GF\s+(\S+)\s+(.*?)\s*$/,Z=/^#=GC\s+(\S+)\s+(.*?)\s*$/,ee=/^#=GS\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,te=/^#=GR\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,ne=/^\s*([^#\s]\S*)\s+(\S+)\s*$/,se=/\S/;function M(r){return j.test(r)}function k(r,e){let n=e??{},t=[],s=null,o=!1,c=r.split(`
+`);for(let i of c){let a;if(j.test(i))s&&t.push(s),s=y(),o=!1;else if(J.test(i))s&&t.push(s),s=null;else if(a=V.exec(i)){s=w(s,!!n.strict);let f=a[1],u=s.gf[f]??=[];f==="NH"&&o&&u.length>0?u[u.length-1]+=a[2]:u.push(a[2]),o=f==="NH"}else if(a=Z.exec(i))s=w(s,!!n.strict),s.gc[a[1]]=(s.gc[a[1]]??"")+a[2];else if(a=ee.exec(i)){s=w(s,!!n.strict);let f=s.gs[a[2]]??=Object.create(null);(f[a[1]]??=[]).push(a[3])}else if(a=te.exec(i)){s=w(s,!!n.strict);let f=s.gr[a[2]]??=Object.create(null);f[a[1]]=(f[a[1]]??"")+a[3]}else if(a=ne.exec(i)){s=w(s,!!n.strict);let f=a[1],u=a[2];s.seqdata[f]===void 0&&(s.seqdata[f]="",s.seqname.push(f)),s.seqdata[f]+=u}else if(se.test(i)&&n.strict)throw new Error("Malformed line")}return s&&t.push(s),t}var g=class extends l{data;MSA;constructor(e,n){let t=k(e),s=t[n]??t[0];if(!s)throw new Error("No alignments found in Stockholm file");super(s.seqname.map(o=>[o,s.seqdata[o]??""])),this.data=t,this.MSA=s}getMSA(){return this.MSA}get alignmentNames(){return this.data.map((e,n)=>e.gf.DE?.[0]??`Alignment ${n+1}`)}getHeader(){let e=this.MSA.gs.AC??{},n=this.MSA.gs.DR??{};return{General:this.MSA.gf,Accessions:Object.fromEntries(Object.entries(e).map(([t,s])=>[t,s[0]])),Dbxref:Object.fromEntries(Object.entries(n).map(([t,s])=>[t,s.join("; ")]))}}getRowData(e){return{name:e,accession:this.MSA.gs.AC?.[e]?.[0],dbxref:this.MSA.gs.DR?.[e]?.join("; ")}}getStructures(){let e=/PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/,n=this.MSA.gs.DR??{},t={};for(let[s,o]of Object.entries(n))for(let c of o){let i=e.exec(c);i&&(t[s]??=[]).push({pdb:i[1].toLowerCase(),chain:i[2],startPos:+i[3],endPos:+i[4]})}return t}getTree(){let e=this.MSA.gf.NH?.[0];return e?T(A(e)):super.getTree()}get seqConsensus(){return this.MSA.gc.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc.SS_cons}get tracks(){let{seq_cons:e,SS_cons:n,...t}=this.MSA.gc;return[{id:"seqConsensus",name:"Sequence consensus",data:e,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:n,customColorScheme:P},...Object.entries(t).map(([s,o])=>({id:`gc-${s}`,name:s,data:o,customColorScheme:G(s)})),...Object.entries(this.MSA.gr).flatMap(([s,o])=>Object.entries(o).map(([c,i])=>({id:`gr-${c}-${s}`,name:`${c} ${s}`,data:i,customColorScheme:G(s),defaultOff:!0})))]}},P={"<":"lightblue","(":"lightblue","[":"lightblue","{":"lightblue",">":"pink",")":"pink","]":"pink","}":"pink"};function G(r){return r==="SS"||r.endsWith("_SS")?P:{}}var oe=/^<(!doctype\s+html|html[\s>])/i,ie=/^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i;function ce(r,e=0,n){let t=r.replace(/^\uFEFF/,"").replaceAll(/\r\n?/g,`
+`).trimStart();if(oe.test(t))throw new Error("Received an HTML page, not an alignment. Check that the URL points at the file itself");if(n==="stockholm")return new g(t,e);if(n==="a3m")return new p(t);if(n==="fasta")return new h(t);if(n==="emf")return new d(t);if(n==="clustal")return new m(t);if(M(t))return new g(t,e);if(R(t)){let o=b(t);return p.sniff(o)?new p(o):new h(o)}if(t.startsWith("SEQ"))return new d(t);if(ie.test(t))return new m(t);let s=t.split(`
+`,1)[0].slice(0,80);throw new Error(s?`Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads "${s}"`:"The alignment file is empty")}function ae(r){return r.replaceAll(/[.-]/g,"")}function D(r){try{return decodeURIComponent(r)}catch{return r}}function fe(r){return r.replace(/^"(.*)"$/,"$1")}function ue(r){if(!r)return{};let e={};for(let n of r.split(";")){let t=n.indexOf("="),s=n.slice(0,t).trim(),o=n.slice(t+1);t!==-1&&s&&o&&(e[s]=o.split(",").map(c=>fe(D(c).trim())).join(" "))}return e}function L(r){if(!r)return[];let e=[];for(let n of r.split(`
+`)){let t=n.trim();if(t.startsWith("##FASTA"))break;t&&!t.startsWith("#")&&t.split("	").length>=8&&e.push(t)}return e.map(n=>{let t=n.split("	"),[s,o,c,i,a,f,u,I]=t,H=t[8];return{...ue(H),seq_id:D(s??""),source:o??"",type:c??"",start:Number(i)||0,end:Number(a)||0,score:Number(f)||0,strand:u??".",phase:I??"."}})}var le=new Set(["gene","CDS","pseudogene","mRNA","transcript","primary_transcript","ncRNA","tRNA","rRNA","snRNA","snoRNA","miRNA","lnc_RNA"]);function pe({type:r,strand:e}){let n=e==="+"?1:e==="-"?-1:void 0;return le.has(r)?n:void 0}var me=new Set(["seq_id","source","type","start","end","score","strand","phase"]);function de(r){let e=Object.entries(r).filter(([n,t])=>!me.has(n)&&typeof t=="string");return e.length>0?Object.fromEntries(e):void 0}var he=/^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/;function ge(r){let e=r.color??r.colour??r.Color??r.Colour;if(!e)return;let n=he.exec(e.trim());return n?`rgb(${n[1]},${n[2]},${n[3]})`:e.trim()}var Se=new Set(["polypeptide","nucleic_acid"]);function U(r){return r.filter(e=>!Se.has(e.type)).map(e=>{let n=e.Name||e.ID||`${e.source}_${e.start}_${e.end}`,t=e.signature_desc||e.Name||n;return{id:e.seq_id,accession:n,name:t,description:e.description||e.Note||e.signature_desc||t,featureType:e.type,start:e.start,end:e.end,strand:pe(e),color:ge(e),attributes:de(e)}})}export{T as a,A as b,ce as c,ae as d,L as e,U as f,B as g};
+//# sourceMappingURL=chunk-DEFUNIWW.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/interProScanToAnnotations.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/annotationsToGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/annotationTextToGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/util.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/BaseMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/fastaRecords.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/A3mMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/ClustalMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/EmfMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/FastaMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/parseNewick.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/stockholmParser.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/StockholmMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/index.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/parseGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/gffToAnnotations.ts"],
+  "sourcesContent": ["import type {\n  Annotation,\n  InterProScanResponse,\n  InterProScanResults,\n} from './types.ts'\n\n/**\n * Key each result by its xref id, which is the row name its annotations attach\n * to. A result without one is dropped rather than keyed `undefined`, which\n * would draw a phantom row's worth of annotations (and rather than throwing,\n * which would lose every other result over one malformed one).\n */\nexport function indexResultsByXref(results: InterProScanResults[]) {\n  return Object.fromEntries(\n    results\n      .map(r => [r.xref[0]?.id, r] as const)\n      .filter((e): e is [string, InterProScanResults] => e[0] !== undefined),\n  )\n}\n\n/**\n * Flatten InterProScan results, keyed by the row name they attach to, into one\n * annotation per signature location.\n *\n * An unintegrated signature has no InterPro `entry` -- MobiDBLite's disorder\n * calls, and many CDD, Pfam and PANTHER hits -- and falling back to the\n * signature's own accession and name is the difference between drawing those\n * and dropping them. Only a signature with no accession at all has nothing to\n * color, filter or label by, and is dropped.\n */\nexport function interProScanToAnnotations(\n  results: Record<string, InterProScanResults>,\n): Annotation[] {\n  return Object.entries(results).flatMap(([id, { matches }]) =>\n    matches.flatMap(({ signature, locations }) => {\n      const { entry } = signature\n      const accession = entry?.accession ?? signature.accession\n      if (!accession) {\n        return []\n      }\n      const name = entry?.name ?? signature.name ?? accession\n      return locations.map(({ start, end, strand }) => ({\n        id,\n        accession,\n        name,\n        description: entry?.description ?? signature.description ?? name,\n        start,\n        end,\n        strand,\n      }))\n    }),\n  )\n}\n\n/**\n * Flatten a whole InterProScan JSON response, resolving each result's row name\n * from its xref.\n */\nexport function interProScanResponseToAnnotations(\n  response: InterProScanResponse,\n): Annotation[] {\n  return interProScanToAnnotations(indexResultsByXref(response.results))\n}\n", "import type { Annotation } from '../types.ts'\n\n/**\n * Write annotations as GFF3, one line per annotation, in list order, with\n * optional `#` comment lines after the version directive saying where they came\n * from.\n *\n * The source column is always `InterProScan`: an Annotation records no source\n * of its own, and the viewer reads a precomputed-lookup GFF by the same rules\n * it reads a real InterProScan run's.\n */\nexport function annotationsToGFF(\n  annotations: Annotation[],\n  header: string[] = [],\n): string {\n  return [\n    '##gff-version 3',\n    ...header.map(line => `# ${line}`),\n    ...annotations.map(annotation => {\n      const { accession, name, description, featureType } = annotation\n      const { id, start, end, strand } = annotation\n      return [\n        id.replaceAll(/[%\\t\\n\\r]/g, encodeURIComponent),\n        'InterProScan',\n        // GFF-sourced annotations carry their original type; writing every\n        // feature back out as protein_match would turn an exon overlay into\n        // generic domains on the next read, losing the numbered-segment\n        // rendering and the gene arrowheads\n        featureType ?? 'protein_match',\n        start,\n        end,\n        '.',\n        strand === undefined ? '.' : strand > 0 ? '+' : '-',\n        '.',\n        [\n          `Name=${encodeURIComponent(accession)}`,\n          `signature_desc=${encodeURIComponent(name)}`,\n          `description=${encodeURIComponent(description)}`,\n        ].join(';'),\n      ].join('\\t')\n    }),\n  ].join('\\n')\n}\n", "import { interProScanResponseToAnnotations } from '../interProScanToAnnotations.ts'\nimport { annotationsToGFF } from './annotationsToGFF.ts'\n\nimport type { InterProScanResponse } from '../types.ts'\n\n/**\n * An annotation file's text as GFF3: GFF passes through, and the JSON an\n * InterProScan run returns converts, taking each result's row from its xref.\n */\nexport function annotationTextToGFF(text: string): string {\n  const trimmed = text.trimStart()\n  if (!trimmed.startsWith('{')) {\n    return text\n  }\n  const response: InterProScanResponse = JSON.parse(trimmed)\n  return annotationsToGFF(interProScanResponseToAnnotations(response))\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", "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 { 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", "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", "import type { GFFRecord } from '../types.ts'\n\n// decodeURIComponent throws on a stray '%' (common in unescaped GFF3 values);\n// fall back to the raw value rather than aborting the whole parse\nfunction safeDecode(val: string) {\n  try {\n    return decodeURIComponent(val)\n  } catch {\n    return val\n  }\n}\n\n// InterProScan quotes some of its values (Ontology_term=\"GO:0008652\",\n// Dbxref=\"InterPro:IPR001048\"), and the quotes are not part of the term\nfunction unquote(val: string) {\n  return val.replace(/^\"(.*)\"$/, '$1')\n}\n\nfunction parseAttributes(col9?: string): Record<string, string> {\n  if (!col9) {\n    return {}\n  }\n  const attributes: Record<string, string> = {}\n  for (const field of col9.split(';')) {\n    const eq = field.indexOf('=')\n    const key = field.slice(0, eq).trim()\n    const val = field.slice(eq + 1)\n    // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a\n    // literal comma encoded as %2C survives the split and isn't mistaken\n    // for a separator\n    if (eq !== -1 && key && val) {\n      attributes[key] = val\n        .split(',')\n        .map(v => unquote(safeDecode(v).trim()))\n        .join(' ')\n    }\n  }\n  return attributes\n}\n\nexport function parseGFF(str?: string): GFFRecord[] {\n  if (!str) {\n    return []\n  }\n  const lines: string[] = []\n  for (const raw of str.split('\\n')) {\n    const line = raw.trim()\n    // InterProScan appends the sequences it scanned; every line past this is\n    // FASTA, and reading it as features gave rows named \">P51587\"\n    if (line.startsWith('##FASTA')) {\n      break\n    }\n    // a feature is nine tab-separated columns, eight of them mandatory; a\n    // FASTA line in a file that omitted the ##FASTA directive is one\n    if (line && !line.startsWith('#') && line.split('\\t').length >= 8) {\n      lines.push(line)\n    }\n  }\n  return lines.map(f => {\n    const parts = f.split('\\t')\n    const [seq_id, source, type, start, end, score, strand, phase] = parts\n    const col9 = parts[8]\n\n    // attributes first, so a column-9 key colliding with a core column (e.g.\n    // \"start=\") can't turn a number field into a string\n    return {\n      ...parseAttributes(col9),\n      seq_id: safeDecode(seq_id ?? ''),\n      source: source ?? '',\n      type: type ?? '',\n      start: Number(start) || 0,\n      end: Number(end) || 0,\n      score: Number(score) || 0,\n      strand: strand ?? '.',\n      phase: phase ?? '.',\n    }\n  })\n}\n", "import type { Annotation, GFFRecord } from '../types.ts'\n\n// Feature types drawn with an arrowhead for their strand. A prokaryotic GFF\n// writes each gene as a CDS row. Exon, UTR and domain features stay blocks,\n// since an exon is a segment of one transcript.\nconst GENE_LEVEL_TYPES = new Set([\n  'gene',\n  'CDS',\n  'pseudogene',\n  'mRNA',\n  'transcript',\n  'primary_transcript',\n  'ncRNA',\n  'tRNA',\n  'rRNA',\n  'snRNA',\n  'snoRNA',\n  'miRNA',\n  'lnc_RNA',\n])\n\n// +1/-1 for a stranded gene-level feature, undefined otherwise (which the\n// renderer draws as a plain block).\nfunction geneStrand({ type, strand }: GFFRecord): number | undefined {\n  const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined\n  return GENE_LEVEL_TYPES.has(type) ? directional : undefined\n}\n\n// The nine columns a feature line holds; every other key of a record came from\n// column 9\nconst GFF_COLUMNS = new Set([\n  'seq_id',\n  'source',\n  'type',\n  'start',\n  'end',\n  'score',\n  'strand',\n  'phase',\n])\n\nfunction attributesOf(record: GFFRecord) {\n  const entries = Object.entries(record).filter(\n    ([key, value]) => !GFF_COLUMNS.has(key) && typeof value === 'string',\n  ) as [string, string][]\n  return entries.length > 0 ? Object.fromEntries(entries) : undefined\n}\n\n// JBrowse and IGV read an RGB triple as well as a named or hex color, and the\n// attribute parser has already turned `255,0,0` into `255 0 0` by splitting on\n// the GFF3 multi-value comma\nconst RGB_TRIPLE = /^(\\d{1,3})[\\s,]+(\\d{1,3})[\\s,]+(\\d{1,3})$/\n\nfunction cssColor(record: GFFRecord) {\n  const value = (record.color ??\n    record.colour ??\n    record.Color ??\n    record.Colour) as string | undefined\n  if (!value) {\n    return undefined\n  }\n  const triple = RGB_TRIPLE.exec(value.trim())\n  return triple ? `rgb(${triple[1]},${triple[2]},${triple[3]})` : value.trim()\n}\n\n// InterProScan describes the sequence it scanned before listing the matches\n// against it. Those lines span the whole row and carry no signature, so they\n// would draw a full-width block labelled by an md5.\nconst WHOLE_SEQUENCE_TYPES = new Set(['polypeptide', 'nucleic_acid'])\n\n/**\n * Convert GFF records to annotations, one per record, in file order.\n *\n * InterProScan's own GFF3 output falls out of the same mapping: it writes\n * `Name` as the signature accession and `signature_desc` as its human-readable\n * name, with domain positions 1-based.\n */\nexport function gffToAnnotations(gffRecords: GFFRecord[]): Annotation[] {\n  return gffRecords\n    .filter(record => !WHOLE_SEQUENCE_TYPES.has(record.type))\n    .map(record => {\n      const accession =\n        (record.Name as string) ||\n        (record.ID as string) ||\n        `${record.source}_${record.start}_${record.end}`\n      const name =\n        (record.signature_desc as string) ||\n        (record.Name as string) ||\n        accession\n      return {\n        id: record.seq_id,\n        accession,\n        name,\n        // not Ontology_term: a GO id list is what the domain is annotated\n        // with, not what it is, and reading it first labelled every\n        // InterProScan domain \"GO:0003677 GO:0006281\"\n        description:\n          (record.description as string) ||\n          (record.Note as string) ||\n          (record.signature_desc as string) ||\n          name,\n        featureType: record.type,\n        start: record.start,\n        end: record.end,\n        strand: geneStrand(record),\n        color: cssColor(record),\n        attributes: attributesOf(record),\n      }\n    })\n}\n"],
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package/dist/chunks/{chunk-YOTSFJMU.js → chunk-ERCMNTEQ.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=chunk-ERCMNTEQ.js.map

package/dist/chunks/{chunk-YOTSFJMU.js.map → chunk-ERCMNTEQ.js.map}

@@ -1,6 +1,6 @@
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package/dist/chunks/{chunk-GDFVLZYX.js → chunk-FEUZKN5V.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-GDFVLZYX.js.map
+import{b as n}from"./chunk-JF6CW6MO.js";import{a as f}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(p(),1),c=i(f(),1);function m({text:t,label:u="Copy to clipboard"}){let[a,r]=(0,e.useState)(!1),o=(0,e.useRef)(void 0);return(0,e.useEffect)(()=>()=>{clearTimeout(o.current)},[]),e.default.createElement(c.Button,{variant:"contained",color:"primary",onClick:()=>{n(typeof t=="string"?t:t()),r(!0),clearTimeout(o.current),o.current=setTimeout(()=>{r(!1)},500)}},a?"Copied!":u)}export{m as a};
+//# sourceMappingURL=chunk-FEUZKN5V.js.map

package/dist/chunks/{chunk-GDFVLZYX.js.map → chunk-FEUZKN5V.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/CopyButton.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/CopyButton.tsx"],
   "sourcesContent": ["import React, { useEffect, useRef, useState } from 'react'\n\nimport { Button } from '@mui/material'\n\nimport copy from '../vendor/copyToClipboard.ts'\n\n/**\n * Copy-to-clipboard button that confirms on the label for a moment. The timer is\n * cleared on unmount, since these live in dialogs the copy itself often closes.\n */\nexport default function CopyButton({\n  text,\n  label = 'Copy to clipboard',\n}: {\n  text: string | (() => string)\n  label?: string\n}) {\n  const [copied, setCopied] = useState(false)\n  const timer = useRef<ReturnType<typeof setTimeout>>(undefined)\n\n  useEffect(\n    () => () => {\n      clearTimeout(timer.current)\n    },\n    [],\n  )\n\n  return (\n    <Button\n      variant=\"contained\"\n      color=\"primary\"\n      onClick={() => {\n        copy(typeof text === 'string' ? text : text())\n        setCopied(true)\n        clearTimeout(timer.current)\n        timer.current = setTimeout(() => {\n          setCopied(false)\n        }, 500)\n      }}\n    >\n      {copied ? 'Copied!' : label}\n    </Button>\n  )\n}\n"],
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package/dist/chunks/{chunk-GIHMPOCO.js → chunk-JF6CW6MO.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-GIHMPOCO.js.map
+//# sourceMappingURL=chunk-JF6CW6MO.js.map

package/dist/chunks/{chunk-GIHMPOCO.js.map → chunk-JF6CW6MO.js.map}

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+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/copyToClipboard.ts"],
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package/dist/chunks/chunk-K55ZVN73.js

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+function k(t){let e=t.split(`
+`).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.push(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,seq:""}});for(let n of s)for(let i=0;i<r.length;i++)o[i].seq+=n[i];return o}function S(t){let e=t.split(`
+`).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(`
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package/dist/chunks/chunk-K55ZVN73.js.map

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+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/emf-js@2.0.0/node_modules/emf-js/src/index.ts", "../../node_modules/.pnpm/clustal-js@2.0.19/node_modules/clustal-js/src/util.ts", "../../node_modules/.pnpm/clustal-js@2.0.19/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. 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