jbrowse-plugin-msaview 5.4.0 → 5.6.0

package/dist/chunks/{chunk-2XCUSA22.js.map → chunk-4TEPHD3L.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["global-externals:@jbrowse/core/util/translateTranscript", "../../src/LaunchMsaView/util.ts", "../../src/LaunchMsaView/components/fetchSeq.ts", "../../src/utils/eutils.ts", "../../src/utils/ncbiOrthologs.ts", "../../node_modules/.pnpm/idb@8.0.4/node_modules/idb/build/index.js", "../../src/utils/idb.ts", "../../src/utils/blastCache.ts", "../../src/utils/taxonomyNames.ts"],
   "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/translateTranscript\"];", "import { getContainingView, sum } from '@jbrowse/core/util'\n\nimport type { AbstractTrackModel, Feature } from '@jbrowse/core/util'\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nexport function getLinearGenomeView(model: AbstractTrackModel) {\n  return getContainingView(model) as LinearGenomeViewModel\n}\n\nfunction isNonEmptyString(v: unknown): v is string {\n  return typeof v === 'string' && v !== ''\n}\n\nfunction uniqueDefined(vals: unknown[]): string[] {\n  return [...new Set(vals.filter(isNonEmptyString))]\n}\n\nfunction joinDefined(sep: string, parts: unknown[]): string {\n  return parts.filter(isNonEmptyString).join(sep)\n}\n\nexport function getTranscriptFeatures(feature: Feature) {\n  // check if we are looking at a 'two-level' or 'three-level' feature by\n  // finding exon/CDS subfeatures. we want to select from transcript names\n  const subfeatures = feature.get('subfeatures') ?? []\n\n  // Check for mRNA/transcript subfeatures (three-level: gene \u2192 mRNA \u2192 CDS)\n  // Filter to only those that have CDS subfeatures (i.e. are coding)\n  const transcripts = subfeatures.filter(\n    (f: Feature) =>\n      (f.get('type') === 'mRNA' || f.get('type') === 'transcript') &&\n      f.get('subfeatures')?.some((s: Feature) => s.get('type') === 'CDS'),\n  )\n  if (transcripts.length > 0) {\n    return transcripts\n  }\n\n  // Has direct CDS children, treat feature itself as the transcript\n  // (two-level: gene \u2192 CDS or mRNA \u2192 CDS)\n  return [feature]\n}\n\nexport function getTranscriptLength(feature: Feature) {\n  const cdsLen = sum(\n    feature\n      .get('subfeatures')\n      ?.filter(f => f.get('type') === 'CDS')\n      .map(s => s.get('end') - s.get('start')) ?? [],\n  )\n  return {\n    len: Math.floor(cdsLen / 3),\n    mod: cdsLen % 3,\n  }\n}\nexport function getId(val?: Feature): string {\n  return val?.id() ?? ''\n}\n\nfunction getMatchableIds(val?: Feature): string[] {\n  return val\n    ? uniqueDefined([\n        val.id(),\n        val.get('name'),\n        val.get('id'),\n        val.get('transcript_id'),\n      ])\n    : []\n}\n\nexport function featureMatchesId(feature: Feature, id: string): boolean {\n  return getMatchableIds(feature).includes(id)\n}\n\nexport function getTranscriptDisplayName(val?: Feature) {\n  return val ? joinDefined(' ', [val.get('name'), val.get('id')]) : ''\n}\n\nexport function getGeneDisplayName(val?: Feature) {\n  return val\n    ? joinDefined(' ', [\n        val.get('gene_name') ?? val.get('name'),\n        val.get('id') ? `(${val.get('id')})` : undefined,\n      ])\n    : ''\n}\n\nexport function getBlastViewTitle(feature: Feature, transcript: Feature) {\n  return `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(transcript)}`\n}\n\nexport function getSortedTranscriptFeatures(feature: Feature) {\n  const transcripts = getTranscriptFeatures(feature)\n  return transcripts.toSorted(\n    (a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len,\n  )\n}\n\n/**\n * A translation as a query, still one residue per codon: g2p numbers codons,\n * and the query row is read through it. So the partial first codon (`&`), an\n * internal stop and an unreadable codon become X, and only what trails the\n * last whole codon is dropped.\n */\nexport function cleanProteinSequence(seq: string) {\n  return seq.replace(/[*&]+$/, '').replaceAll(/[*&]/g, 'X')\n}\n\nexport function getGeneIdentifiers(feature: Feature): string[] {\n  return uniqueDefined([\n    feature.id(),\n    feature.get('id'),\n    feature.get('name'),\n    feature.get('gene_id'),\n    feature.get('gene_name'),\n  ])\n}\n", "import { getConf } from '@jbrowse/core/configuration'\n\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\nexport async function fetchSeq({\n  start,\n  end,\n  refName,\n  session,\n  assemblyName,\n}: {\n  start: number\n  end: number\n  refName: string\n  assemblyName: string\n  session: AbstractSessionModel\n}) {\n  const { assemblyManager, rpcManager } = session\n  const assembly = await assemblyManager.waitForAssembly(assemblyName)\n  if (!assembly) {\n    throw new Error('assembly not found')\n  }\n  const feats = await rpcManager.call('getSequence', 'CoreGetFeatures', {\n    adapterConfig: getConf(assembly, ['sequence', 'adapter']),\n    regions: [\n      {\n        start,\n        end,\n        refName: assembly.getCanonicalRefName(refName) ?? refName,\n        assemblyName,\n      },\n    ],\n  })\n  return {\n    seq: (feats[0]?.get('seq') as string | undefined) ?? '',\n    // travels with the sequence because the caller needs both to translate, and\n    // resolving the assembly twice to get them is the shape that lost it\n    assemblyGeneticCodeId: assembly.getGeneticCodeId(refName),\n  }\n}\n", "import { jsonfetch, textfetch, timeout } from './fetch'\n\n// NCBI asks that programmatic E-utilities requests identify themselves with a\n// tool name and contact email so they can reach out before throttling, rather\n// than silently rate-limiting. https://www.ncbi.nlm.nih.gov/books/NBK25497/\nconst NCBI_TOOL = 'jbrowse-plugin-msaview'\nconst NCBI_EMAIL = 'jbrowse2@berkeley.edu'\n\nconst EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils'\n\ntype Endpoint = 'efetch' | 'esearch' | 'esummary'\n\nfunction identified(params: Record<string, string>) {\n  return new URLSearchParams({ ...params, tool: NCBI_TOOL, email: NCBI_EMAIL })\n}\n\nexport function eutilsUrl(endpoint: Endpoint, params: Record<string, string>) {\n  return `${EUTILS}/${endpoint}.fcgi?${identified(params).toString()}`\n}\n\nexport function efetchUrl(params: Record<string, string>) {\n  return eutilsUrl('efetch', params)\n}\n\n/**\n * The same request as a POST body. An `id` list of a few hundred accessions\n * exceeds what a URL carries \u2014 865 of them is ~13KB \u2014 and NCBI documents POST\n * as the route above about 200 ids. eutils sends `ACAO: *` on both verbs.\n */\nexport function efetchPost(params: Record<string, string>) {\n  return [\n    `${EUTILS}/efetch.fcgi`,\n    { method: 'POST', body: identified(params) },\n  ] as const\n}\n\n/**\n * eutils allows 3 requests a second without an API key and answers a burst\n * over that with no `Access-Control-Allow-Origin`, which the browser reports as\n * a CORS failure. Every eutils request takes the next start slot, so however\n * many callers ask at once the requests go out under the limit.\n */\nexport const EUTILS_SPACING_MS = 350\n\nlet nextSlot = 0\n\nasync function eutilsSlot(signal?: AbortSignal | null) {\n  const now = Date.now()\n  const start = Math.max(now, nextSlot)\n  nextSlot = start + EUTILS_SPACING_MS\n  if (start > now) {\n    try {\n      await timeout(start - now, signal ?? undefined)\n    } catch (e) {\n      if (nextSlot === start + EUTILS_SPACING_MS) {\n        nextSlot = start\n      }\n      throw e\n    }\n  }\n}\n\nexport async function eutilsText(url: string, init?: RequestInit) {\n  await eutilsSlot(init?.signal)\n  return textfetch(url, init)\n}\n\nexport async function eutilsJson<T>(url: string, init?: RequestInit) {\n  await eutilsSlot(init?.signal)\n  return jsonfetch<T>(url, init)\n}\n\nconst namedEntities: Record<string, string> = {\n  amp: '&',\n  apos: \"'\",\n  gt: '>',\n  lt: '<',\n  quot: '\"',\n}\n\n/** Text lifted out of eutils XML still carries its escapes: `5&apos;-3&apos;`. */\nexport function decodeXmlEntities(text: string) {\n  return text.replaceAll(\n    /&(#x[\\da-f]+|#\\d+|[a-z]+);/gi,\n    (entity, name: string) =>\n      name.startsWith('#x') || name.startsWith('#X')\n        ? String.fromCodePoint(Number.parseInt(name.slice(2), 16))\n        : name.startsWith('#')\n          ? String.fromCodePoint(Number(name.slice(1)))\n          : (namedEntities[name] ?? entity),\n  )\n}\n", "// Homolog discovery WITHOUT a search job.\n//\n// The BLAST path answers \"what looks like this sequence\", which is not the\n// question an MSA row set wants \u2014 it wants \"what is homologous to this gene,\n// one per species, labelled by species\". BLAST then costs 10+ minutes to\n// return a redundant, accession-labelled hit list that has to be deduplicated\n// before it reads. NCBI has already computed the answer: the Datasets\n// orthologs endpoint returns one ortholog gene per species, instantly.\n//\n// gene symbol -> gene id -> orthologs -> a representative protein each ->\n// sequences, all from NCBI, in a handful of requests. The caller aligns them\n// (EBI Clustal Omega, ~10s) and overlays CDD domains, which are already baked\n// into the GenPept records (see ncbiDomains.ts).\n//\n// Mirrors jb2hubs' website/src/components/proteinMsa.ts assembler, trimmed to\n// what the launch dialog needs and using this plugin's fetch/eutils helpers.\n\nimport {\n  efetchPost,\n  efetchUrl,\n  eutilsJson,\n  eutilsText,\n  eutilsUrl,\n} from './eutils'\nimport { HttpError, jsonfetch } from './fetch'\n\n// v2, not v2alpha: the alpha path still answers /orthologs but 404s\n// /product_report, so an assembler pointed at it silently resolves zero\n// representative proteins and reports \"no orthologs\" for every gene.\nconst DATASETS = 'https://api.ncbi.nlm.nih.gov/datasets/v2'\n\n// NCBI's ortholog report IS the species panel. There is no list here to keep in\n// step with what NCBI knows, and the panel widens by itself as NCBI annotates\n// more genomes.\n//\n// It used to be a hand-written 23-species list intersected with the report, and\n// the intersection is what made the alignment thin: NCBI publishes 165 orthologs\n// for human NLRP1 and 865 for CFTR, so the list kept 12 of the first and 19 of\n// the second. It also carried four species -- fruitfly, yeast, C. elegans and\n// arabidopsis -- that the endpoint has never once returned for a human gene:\n// checked against NLRP1, TP53, ACTB, BRCA1, PIK3CA, APOE and NOTCH1, whose fly\n// ortholog is famous and still absent. NCBI's ortholog sets are vertebrate\n// scoped.\n//\n// The report's OWN order is the ladder the list was hand-built to approximate,\n// and it is per gene. CFTR opens human, mouse, rat, zebrafish, pig, sheep,\n// rabbit, chicken, cattle, ferret, dog, rhesus; NLRP1, which has no ortholog\n// outside placental mammals, opens human, mouse, rhesus, shrew mouse, chimp,\n// dog, cattle, horse. So `limit` takes a prefix and never needs a rank table.\n//\n// The rows are SUBMITTED in that order, not drawn in it -- the view lays rows out\n// by the guide tree the aligner returns.\n//\n// What limits the row count is the aligner, and it is linear in rows at roughly\n// half a second each for a ~1400aa protein: 165 NLRP1 orthologs align at EBI in\n// 88s, 865 CFTR orthologs in 407s. `defaultMaxSpecies` keeps a default run under\n// a minute; EBI's own ceiling is 4000 sequences and 4MB, which even CFTR's full\n// set (1.3MB) sits inside.\nexport const defaultMaxSpecies = 100\n\nexport interface OrthologRow {\n  taxId: number\n  /** single-token id used identically in the FASTA, the tree and the domain GFF */\n  label: string\n  scientificName: string\n  commonName?: string\n  geneId: string\n  /** accession.version */\n  protein: string\n  sequence: string\n}\n\n/**\n * A candidate gene reference as the ortholog services know it: a GFF ID prefix\n * (gene:TP53) and a version suffix (NM_000546.6) stripped off. Shared with\n * pantherOrthologs, which asks PANTHER the same question with the same\n * candidates.\n */\nexport function cleanGeneCandidate(raw: string) {\n  return raw\n    .trim()\n    .replace(/^\\w+:/, '')\n    .replace(/\\.\\d+$/, '')\n}\n\nexport interface SymbolCandidate {\n  gene_id?: string\n  symbol?: string\n  synonyms?: string[]\n}\n\n/**\n * NCBI's symbol lookups match aliases as well as symbols and rank neither\n * first: `TTN` in human answers TTR (transthyretin, whose alias it is) ahead of\n * titin, from Datasets and from an esearch `[Gene Name]` alike. Case decides\n * before a case-blind match, because fly `Dl` (Delta) and `dl` (dorsal) differ\n * by it alone. The first hit stands when nothing matches, which is what keeps\n * an alias like `p53` working. The same rule as jb2hubs' orthologSet.ts.\n */\nexport function pickBySymbol(query: string, candidates: SymbolCandidate[]) {\n  const lower = query.toLowerCase()\n  const exact =\n    candidates.find(c => c.symbol === query) ??\n    candidates.find(c => c.synonyms?.includes(query)) ??\n    candidates.find(c => c.symbol?.toLowerCase() === lower)\n  return (exact ?? candidates[0])?.gene_id\n}\n\n/** Datasets answers an unknown symbol with `{}` and an unroutable one with a 404 */\nasync function symbolCandidates(\n  symbol: string,\n  taxId: number,\n  signal?: AbortSignal,\n) {\n  try {\n    const json = await jsonfetch<{ reports?: { gene?: SymbolCandidate }[] }>(\n      `${DATASETS}/gene/symbol/${encodeURIComponent(symbol)}/taxon/${taxId}`,\n      { signal },\n    )\n    return (json.reports ?? []).flatMap(r => (r.gene ? [r.gene] : []))\n  } catch (e) {\n    if (e instanceof HttpError && (e.status === 400 || e.status === 404)) {\n      return []\n    }\n    throw e\n  }\n}\n\nasync function searchGeneName(\n  name: string,\n  taxId: number,\n  signal?: AbortSignal,\n) {\n  const json = await eutilsJson<{\n    esearchresult?: { idlist?: string[] }\n  }>(\n    eutilsUrl('esearch', {\n      db: 'gene',\n      term: `${name}[Gene Name] AND ${taxId}[taxid]`,\n      retmode: 'json',\n      retmax: '1',\n    }),\n    { signal },\n  )\n  return json.esearchresult?.idlist?.[0]\n}\n\n/**\n * A free-text gene reference -> NCBI gene id. Several candidate identifiers\n * are tried in order, because a JBrowse feature carries whatever its GFF/BigBed\n * had \u2014 `id()`, `name`, `gene_name` \u2014 and only some of those are real symbols.\n * `gene:TP53` and `TP53` are one search. Each is asked of Datasets, whose\n * candidates `pickBySymbol` ranks, and then of esearch, which also reaches\n * descriptions.\n *\n * A bare number is taken as the id itself only when no name resolves, since\n * nothing checks whose gene it is: a GFF `ID=12345` beside `Name=TP53` would\n * otherwise align some other organism's orthologs.\n */\nexport async function resolveGeneId(\n  candidates: string[],\n  taxId: number,\n  signal?: AbortSignal,\n): Promise<{ geneId: string; matched: string } | undefined> {\n  const asked = new Set<string>()\n  const queries = candidates.map(c => c.trim())\n  const isId = (query: string) => /^\\d+$/.test(query)\n  for (const query of queries.filter(q => !isId(q))) {\n    const cleaned = cleanGeneCandidate(query)\n    if (!cleaned || asked.has(cleaned)) {\n      continue\n    }\n    asked.add(cleaned)\n    const geneId =\n      pickBySymbol(cleaned, await symbolCandidates(cleaned, taxId, signal)) ??\n      (await searchGeneName(cleaned, taxId, signal))\n    if (geneId) {\n      return { geneId, matched: cleaned }\n    }\n  }\n  const id = queries.find(isId)\n  return id ? { geneId: id, matched: id } : undefined\n}\n\ninterface OrthologReport {\n  reports?: {\n    gene?: {\n      gene_id?: string\n      tax_id?: string | number\n      taxname?: string\n      common_name?: string\n    }\n  }[]\n}\n\n/**\n * One ortholog gene per species, in NCBI's report order, capped at `limit`.\n *\n * `taxa` narrows the set when a caller wants specific species; omitted, every\n * species NCBI has an ortholog for is a candidate. `exclude` drops the query\n * taxon, which already has its own `<species>_query` row.\n */\nexport async function fetchOrthologGenes(\n  geneId: string,\n  {\n    taxa,\n    exclude,\n    limit = defaultMaxSpecies,\n    signal,\n  }: {\n    taxa?: Set<number>\n    exclude?: number\n    limit?: number\n    signal?: AbortSignal\n  } = {},\n) {\n  const json = await jsonfetch<OrthologReport>(\n    `${DATASETS}/gene/id/${geneId}/orthologs?returned_content=COMPLETE`,\n    { signal },\n  )\n  const byTaxon = new Map<\n    number,\n    {\n      taxId: number\n      geneId: string\n      scientificName: string\n      commonName?: string\n    }\n  >()\n  for (const { gene } of json.reports ?? []) {\n    const taxId = Number(gene?.tax_id)\n    if (\n      gene?.gene_id &&\n      taxId !== exclude &&\n      (taxa?.has(taxId) ?? true) &&\n      !byTaxon.has(taxId)\n    ) {\n      byTaxon.set(taxId, {\n        taxId,\n        geneId: gene.gene_id,\n        scientificName: gene.taxname ?? String(taxId),\n        commonName: gene.common_name,\n      })\n    }\n    if (byTaxon.size >= limit) {\n      break\n    }\n  }\n  return [...byTaxon.values()]\n}\n\ninterface ProductReport {\n  reports?: {\n    product?: {\n      gene_id?: string\n      transcripts?: {\n        select_category?: string\n        protein?: { accession_version?: string; length?: number }\n      }[]\n    }\n  }[]\n}\n\n// Two ceilings sit between a gene id list and its product report, and both fail\n// by returning less rather than by erroring, so a caller that ignores them just\n// draws a thinner alignment.\n//\n// The ids go in the URL PATH, and NCBI answers HTTP 414 above roughly 8KB of\n// them -- CFTR's 865 orthologs join to 8609 characters and 414 on the nose.\n// `PRODUCT_REPORT_CHUNK` keeps a request well inside that.\n//\n// Then the endpoint paginates at 20 with the count in `total_count` and the rest\n// behind `next_page_token`, which is invisible to a caller reading `reports`.\n// `page_size` covers a chunk in one request. The old 23-species panel never\n// reached this: the query taxon is excluded and NCBI has no ortholog for the\n// four invertebrate entries, so its ceiling was 19.\nconst PRODUCT_REPORT_CHUNK = 150\n\n/**\n * geneId -> representative protein accession: MANE Select where flagged, else\n * the longest isoform. A stable, comparable choice across species \u2014 picking\n * \"the first\" would silently vary with NCBI's ordering.\n */\nexport async function fetchRepresentativeProteins(\n  geneIds: string[],\n  signal?: AbortSignal,\n) {\n  const byGene = new Map<string, string>()\n  for (let i = 0; i < geneIds.length; i += PRODUCT_REPORT_CHUNK) {\n    const chunk = geneIds.slice(i, i + PRODUCT_REPORT_CHUNK)\n    const json = await jsonfetch<ProductReport>(\n      `${DATASETS}/gene/id/${chunk.join(',')}/product_report?page_size=${chunk.length}`,\n      { signal },\n    )\n    for (const { product } of json.reports ?? []) {\n      const candidates = (product?.transcripts ?? [])\n        .map(t => ({\n          acc: t.protein?.accession_version,\n          len: t.protein?.length ?? 0,\n          mane: /select/i.test(t.select_category ?? ''),\n        }))\n        .filter(\n          (c): c is { acc: string; len: number; mane: boolean } => !!c.acc,\n        )\n      const best =\n        candidates.find(c => c.mane) ??\n        [...candidates].sort((a, b) => b.len - a.len).at(0)\n      if (product?.gene_id && best) {\n        byGene.set(product.gene_id, best.acc)\n      }\n    }\n  }\n  return byGene\n}\n\n/** accession (first header token) -> ungapped sequence, from a multi-FASTA. */\nexport function parseFasta(text: string) {\n  const map = new Map<string, string>()\n  let acc: string | undefined\n  let buf: string[] = []\n  for (const line of text.split('\\n')) {\n    if (line.startsWith('>')) {\n      if (acc) {\n        map.set(acc, buf.join(''))\n      }\n      acc = line.slice(1).split(/\\s+/)[0]\n      buf = []\n    } else {\n      buf.push(line.trim())\n    }\n  }\n  if (acc) {\n    map.set(acc, buf.join(''))\n  }\n  return map\n}\n\nfunction sanitize(name: string) {\n  return name.replace(/[^A-Za-z0-9]+/g, '_').replace(/^_+|_+$/g, '')\n}\n\n/**\n * Sanitized, unique single-token labels used identically in the FASTA headers,\n * the tree leaf names and the domain GFF seq_ids \u2014 that identity is how the\n * viewer pairs a tree leaf to its alignment row to its domain track. Collisions\n * get a numeric suffix rather than silently overwriting a row, and the suffix\n * climbs past labels already emitted: a species genuinely named `human_2` would\n * otherwise take the label the second `human` is about to get, merging two rows\n * into one.\n */\nexport function dedupeLabels(names: string[]) {\n  const used = new Set<string>()\n  return names.map(name => {\n    const base = sanitize(name) || 'row'\n    let label = base\n    let n = 1\n    while (used.has(label)) {\n      n += 1\n      label = `${base}_${n}`\n    }\n    used.add(label)\n    return label\n  })\n}\n\n/**\n * The representative protein for a single gene, with its sequence. Used to\n * decide whether the user's own translated transcript is byte-identical to the\n * RefSeq protein \u2014 if it is, that accession's precomputed CDD domains apply to\n * the query row exactly, and if it isn't, they would land at an offset.\n */\nexport async function fetchProteinForGene(\n  geneId: string,\n  signal?: AbortSignal,\n) {\n  const acc = (await fetchRepresentativeProteins([geneId], signal)).get(geneId)\n  if (!acc) {\n    return undefined\n  }\n  const seq = parseFasta(\n    await eutilsText(\n      efetchUrl({ db: 'protein', id: acc, rettype: 'fasta', retmode: 'text' }),\n      { signal },\n    ),\n  ).get(acc)\n  return seq ? { accession: acc, sequence: seq } : undefined\n}\n\n/**\n * The whole NCBI half of the pipeline: gene -> ortholog rows carrying labels,\n * accessions and sequences. Everything here is a precomputed lookup, so this\n * returns in seconds rather than the 10+ minutes a BLAST submission costs.\n */\nexport async function fetchOrthologRows({\n  geneId,\n  taxa,\n  exclude,\n  limit,\n  onProgress,\n  signal,\n}: {\n  geneId: string\n  taxa?: Set<number>\n  exclude?: number\n  limit?: number\n  onProgress: (arg: string) => void\n  signal?: AbortSignal\n}): Promise<OrthologRow[]> {\n  onProgress('Finding orthologs across species...')\n  const genes = await fetchOrthologGenes(geneId, {\n    taxa,\n    exclude,\n    limit,\n    signal,\n  })\n  if (genes.length < 2) {\n    throw new Error(\n      `Only ${genes.length} ortholog(s) found for this gene \u2014 not enough to align`,\n    )\n  }\n\n  onProgress('Selecting a representative protein per species...')\n  const proteinByGene = await fetchRepresentativeProteins(\n    genes.map(g => g.geneId),\n    signal,\n  )\n  const withProtein = genes.filter(g => proteinByGene.has(g.geneId))\n  if (withProtein.length < 2) {\n    throw new Error(\n      'Could not resolve representative proteins for the orthologs',\n    )\n  }\n\n  onProgress(`Fetching ${withProtein.length} protein sequences...`)\n  const accessions = withProtein.map(g => proteinByGene.get(g.geneId)!)\n  const [efetch, init] = efetchPost({\n    db: 'protein',\n    id: accessions.join(','),\n    rettype: 'fasta',\n    retmode: 'text',\n  })\n  const seqByAcc = parseFasta(await eutilsText(efetch, { ...init, signal }))\n\n  const labels = dedupeLabels(\n    withProtein.map(g => g.commonName ?? g.scientificName),\n  )\n  const rows = withProtein\n    .map((g, i) => {\n      const protein = proteinByGene.get(g.geneId)!\n      return {\n        taxId: g.taxId,\n        label: labels[i]!,\n        scientificName: g.scientificName,\n        commonName: g.commonName,\n        geneId: g.geneId,\n        protein,\n        sequence: seqByAcc.get(protein) ?? '',\n      }\n    })\n    .filter(r => r.sequence)\n  if (rows.length < 2) {\n    throw new Error('Could not fetch protein sequences for the orthologs')\n  }\n  return rows\n}\n", "const instanceOfAny = (object, constructors) => constructors.some((c) => object instanceof c);\n\nlet idbProxyableTypes;\nlet cursorAdvanceMethods;\n// This is a function to prevent it throwing up in node environments.\nfunction getIdbProxyableTypes() {\n    return (idbProxyableTypes ||\n        (idbProxyableTypes = [\n            IDBIndex,\n            IDBObjectStore,\n            IDBCursor,\n            IDBDatabase,\n            IDBTransaction,\n        ]));\n}\n// This is a function to prevent it throwing up in node environments.\nfunction getCursorAdvanceMethods() {\n    return (cursorAdvanceMethods ||\n        (cursorAdvanceMethods = ['advance', 'continue', 'continuePrimaryKey'].map((method) => IDBCursor.prototype[method])));\n}\nconst transactionDoneMap = new WeakMap();\nconst transformCache = new WeakMap();\nconst reverseTransformCache = new WeakMap();\nfunction promisifyRequest(request) {\n    const promise = new Promise((resolve, reject) => {\n        const unlisten = () => {\n            request.removeEventListener('success', success);\n            request.removeEventListener('error', error);\n        };\n        const success = () => {\n            resolve(wrap(request.result));\n            unlisten();\n        };\n        const error = () => {\n            reject(request.error);\n            unlisten();\n        };\n        request.addEventListener('success', success);\n        request.addEventListener('error', error);\n    });\n    // This mapping exists in reverseTransformCache but doesn't exist in transformCache. This\n    // is because we create many promises from a single IDBRequest.\n    reverseTransformCache.set(promise, request);\n    return promise;\n}\nfunction cacheDonePromiseForTransaction(tx) {\n    // Early bail if we've already created a done promise for this transaction.\n    if (transactionDoneMap.has(tx))\n        return;\n    const done = new Promise((resolve, reject) => {\n        const unlisten = () => {\n            tx.removeEventListener('complete', complete);\n            tx.removeEventListener('error', error);\n            tx.removeEventListener('abort', error);\n        };\n        const complete = () => {\n            resolve();\n            unlisten();\n        };\n        const error = () => {\n            reject(tx.error || new DOMException('AbortError', 'AbortError'));\n            unlisten();\n        };\n        tx.addEventListener('complete', complete);\n        tx.addEventListener('error', error);\n        tx.addEventListener('abort', error);\n    });\n    // Cache it for later retrieval.\n    transactionDoneMap.set(tx, done);\n}\nlet idbProxyTraps = {\n    get(target, prop, receiver) {\n        if (target instanceof IDBTransaction) {\n            // Special handling for transaction.done.\n            if (prop === 'done')\n                return transactionDoneMap.get(target);\n            // Make tx.store return the only store in the transaction, or undefined if there are many.\n            if (prop === 'store') {\n                return receiver.objectStoreNames[1]\n                    ? undefined\n                    : receiver.objectStore(receiver.objectStoreNames[0]);\n            }\n        }\n        // Else transform whatever we get back.\n        return wrap(target[prop]);\n    },\n    set(target, prop, value) {\n        target[prop] = value;\n        return true;\n    },\n    has(target, prop) {\n        if (target instanceof IDBTransaction &&\n            (prop === 'done' || prop === 'store')) {\n            return true;\n        }\n        return prop in target;\n    },\n};\nfunction replaceTraps(callback) {\n    idbProxyTraps = callback(idbProxyTraps);\n}\nfunction wrapFunction(func) {\n    // Due to expected object equality (which is enforced by the caching in `wrap`), we\n    // only create one new func per func.\n    // Cursor methods are special, as the behaviour is a little more different to standard IDB. In\n    // IDB, you advance the cursor and wait for a new 'success' on the IDBRequest that gave you the\n    // cursor. It's kinda like a promise that can resolve with many values. That doesn't make sense\n    // with real promises, so each advance methods returns a new promise for the cursor object, or\n    // undefined if the end of the cursor has been reached.\n    if (getCursorAdvanceMethods().includes(func)) {\n        return function (...args) {\n            // Calling the original function with the proxy as 'this' causes ILLEGAL INVOCATION, so we use\n            // the original object.\n            func.apply(unwrap(this), args);\n            return wrap(this.request);\n        };\n    }\n    return function (...args) {\n        // Calling the original function with the proxy as 'this' causes ILLEGAL INVOCATION, so we use\n        // the original object.\n        return wrap(func.apply(unwrap(this), args));\n    };\n}\nfunction transformCachableValue(value) {\n    if (typeof value === 'function')\n        return wrapFunction(value);\n    // This doesn't return, it just creates a 'done' promise for the transaction,\n    // which is later returned for transaction.done (see idbObjectHandler).\n    if (value instanceof IDBTransaction)\n        cacheDonePromiseForTransaction(value);\n    if (instanceOfAny(value, getIdbProxyableTypes()))\n        return new Proxy(value, idbProxyTraps);\n    // Return the same value back if we're not going to transform it.\n    return value;\n}\nfunction wrap(value) {\n    // We sometimes generate multiple promises from a single IDBRequest (eg when cursoring), because\n    // IDB is weird and a single IDBRequest can yield many responses, so these can't be cached.\n    if (value instanceof IDBRequest)\n        return promisifyRequest(value);\n    // If we've already transformed this value before, reuse the transformed value.\n    // This is faster, but it also provides object equality.\n    if (transformCache.has(value))\n        return transformCache.get(value);\n    const newValue = transformCachableValue(value);\n    // Not all types are transformed.\n    // These may be primitive types, so they can't be WeakMap keys.\n    if (!Object.is(newValue, value)) {\n        transformCache.set(value, newValue);\n        reverseTransformCache.set(newValue, value);\n    }\n    return newValue;\n}\nconst unwrap = (value) => reverseTransformCache.get(value);\n\n/**\n * Open a database.\n *\n * @param name Name of the database.\n * @param version Schema version.\n * @param callbacks Additional callbacks.\n */\nfunction openDB(name, version, { blocked, upgrade, blocking, terminated } = {}) {\n    const request = indexedDB.open(name, version);\n    const openPromise = wrap(request);\n    if (upgrade) {\n        request.addEventListener('upgradeneeded', (event) => {\n            upgrade(wrap(request.result), event.oldVersion, event.newVersion, wrap(request.transaction), event);\n        });\n    }\n    if (blocked) {\n        request.addEventListener('blocked', (event) => blocked(\n        // Casting due to https://github.com/microsoft/TypeScript-DOM-lib-generator/pull/1405\n        event.oldVersion, event.newVersion, event));\n    }\n    openPromise\n        .then((db) => {\n        if (terminated)\n            db.addEventListener('close', () => terminated());\n        if (blocking) {\n            db.addEventListener('versionchange', (event) => blocking(event.oldVersion, event.newVersion, event));\n        }\n    })\n        .catch(() => { });\n    return openPromise;\n}\n/**\n * Delete a database.\n *\n * @param name Name of the database.\n */\nfunction deleteDB(name, { blocked } = {}) {\n    const request = indexedDB.deleteDatabase(name);\n    if (blocked) {\n        request.addEventListener('blocked', (event) => blocked(\n        // Casting due to https://github.com/microsoft/TypeScript-DOM-lib-generator/pull/1405\n        event.oldVersion, event));\n    }\n    return wrap(request).then(() => undefined);\n}\n\nconst readMethods = ['get', 'getKey', 'getAll', 'getAllKeys', 'count'];\nconst writeMethods = ['put', 'add', 'delete', 'clear'];\nconst cachedMethods = {};\nfunction getMethod(target, prop) {\n    if (!(target instanceof IDBDatabase &&\n        !(prop in target) &&\n        typeof prop === 'string')) {\n        return;\n    }\n    if (cachedMethods[prop])\n        return cachedMethods[prop];\n    const targetFuncName = prop.replace(/FromIndex$/, '');\n    const useIndex = prop !== targetFuncName;\n    const isWrite = writeMethods.includes(targetFuncName);\n    if (\n    // Bail if the target doesn't exist on the target. Eg, getAll isn't in Edge.\n    !(targetFuncName in (useIndex ? IDBIndex : IDBObjectStore).prototype) ||\n        !(isWrite || readMethods.includes(targetFuncName))) {\n        return;\n    }\n    const method = async function (storeName, ...args) {\n        // isWrite ? 'readwrite' : undefined gzipps better, but fails in Edge :(\n        const tx = this.transaction(storeName, isWrite ? 'readwrite' : 'readonly');\n        let target = tx.store;\n        if (useIndex)\n            target = target.index(args.shift());\n        // Must reject if op rejects.\n        // If it's a write operation, must reject if tx.done rejects.\n        // Must reject with op rejection first.\n        // Must resolve with op value.\n        // Must handle both promises (no unhandled rejections)\n        return (await Promise.all([\n            target[targetFuncName](...args),\n            isWrite && tx.done,\n        ]))[0];\n    };\n    return (cachedMethods[prop] = method);\n}\nreplaceTraps((oldTraps) => ({\n    ...oldTraps,\n    get: (target, prop, receiver) => getMethod(target, prop) || oldTraps.get(target, prop, receiver),\n    has: (target, prop) => !!getMethod(target, prop) || oldTraps.has(target, prop),\n}));\n\nconst advanceMethodProps = ['advance', 'continue', 'continuePrimaryKey'];\nconst methodMap = {};\nconst advanceResults = new WeakMap();\nconst ittrProxiedCursorToOriginalProxy = new WeakMap();\nconst cursorIteratorTraps = {\n    get(target, prop) {\n        if (!advanceMethodProps.includes(prop))\n            return target[prop];\n        let cachedFunc = methodMap[prop];\n        if (!cachedFunc) {\n            cachedFunc = methodMap[prop] = function (...args) {\n                advanceResults.set(this, ittrProxiedCursorToOriginalProxy.get(this)[prop](...args));\n            };\n        }\n        return cachedFunc;\n    },\n};\nasync function* iterate(...args) {\n    // tslint:disable-next-line:no-this-assignment\n    let cursor = this;\n    if (!(cursor instanceof IDBCursor)) {\n        cursor = await cursor.openCursor(...args);\n    }\n    if (!cursor)\n        return;\n    cursor = cursor;\n    const proxiedCursor = new Proxy(cursor, cursorIteratorTraps);\n    ittrProxiedCursorToOriginalProxy.set(proxiedCursor, cursor);\n    // Map this double-proxy back to the original, so other cursor methods work.\n    reverseTransformCache.set(proxiedCursor, unwrap(cursor));\n    while (cursor) {\n        yield proxiedCursor;\n        // If one of the advancing methods was not called, call continue().\n        cursor = await (advanceResults.get(proxiedCursor) || cursor.continue());\n        advanceResults.delete(proxiedCursor);\n    }\n}\nfunction isIteratorProp(target, prop) {\n    return ((prop === Symbol.asyncIterator &&\n        instanceOfAny(target, [IDBIndex, IDBObjectStore, IDBCursor])) ||\n        (prop === 'iterate' && instanceOfAny(target, [IDBIndex, IDBObjectStore])));\n}\nreplaceTraps((oldTraps) => ({\n    ...oldTraps,\n    get(target, prop, receiver) {\n        if (isIteratorProp(target, prop))\n            return iterate;\n        return oldTraps.get(target, prop, receiver);\n    },\n    has(target, prop) {\n        return isIteratorProp(target, prop) || oldTraps.has(target, prop);\n    },\n}));\n\nexport { deleteDB, openDB, unwrap, wrap };\n", "import { openDB } from 'idb'\n\nimport type { DBSchema, IDBPDatabase, OpenDBCallbacks } from 'idb'\n\n/**\n * Memoized `openDB` for a typed schema, shared by this plugin's caches.\n *\n * Callers share one connection. The opener forgets it whenever it stops being\n * usable, so the next call opens a fresh one instead of replaying a rejection\n * or waiting on a dead handle: when the open fails (IndexedDB is unavailable in\n * some private-browsing modes), when another tab is blocked upgrading the\n * database and this connection steps aside for it, and when the browser\n * terminates the connection.\n *\n * An open blocked by another tab's older connection rejects rather than waiting\n * for that tab to close, which may never happen, since a build that predates\n * `blocking` never steps aside.\n *\n * Passing a DBSchema is what keeps `get`/`getAll` from returning `any`: with an\n * untyped database every cached record reaches the UI unchecked.\n */\nexport function createDbOpener<T extends DBSchema>(\n  name: string,\n  version: number,\n  upgrade: OpenDBCallbacks<T>['upgrade'],\n) {\n  let dbPromise: Promise<IDBPDatabase<T>> | undefined\n  const forget = () => {\n    dbPromise = undefined\n  }\n  return () => {\n    dbPromise ??= new Promise<IDBPDatabase<T>>((resolve, reject) => {\n      let gaveUp = false\n      openDB<T>(name, version, {\n        upgrade,\n        blocked(currentVersion) {\n          gaveUp = true\n          reject(\n            new Error(\n              `${name} is held open at version ${currentVersion} by another tab`,\n            ),\n          )\n        },\n        blocking(_currentVersion, _blockedVersion, event) {\n          ;(event.target as IDBDatabase).close()\n          forget()\n        },\n        terminated: forget,\n      }).then(db => {\n        if (gaveUp) {\n          db.close()\n        } else {\n          resolve(db)\n        }\n      }, reject)\n    }).catch((e: unknown) => {\n      forget()\n      throw e\n    })\n    return dbPromise\n  }\n}\n\n/**\n * Run a cache operation that the caller can do without. A cache only saves\n * work, so a read that fails answers `fallback` (a miss) and a write that fails\n * is skipped: neither may cost the user a search that already finished.\n */\nexport async function bestEffort<R>(\n  what: string,\n  operation: () => Promise<R>,\n  fallback: R,\n) {\n  try {\n    return await operation()\n  } catch (e) {\n    console.warn(`[msaview] ${what} failed, continuing without it:`, e)\n    return fallback\n  }\n}\n", "import { defaultMaxHits } from '../LaunchMsaView/components/BlastQuery/consts'\nimport { bestEffort, createDbOpener } from './idb'\n\nimport type {\n  BlastDatabase,\n  MsaAlgorithm,\n  PhmmerDatabase,\n  SearchProgram,\n} from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { DBSchema, IDBPDatabase } from 'idb'\n\nconst DB_NAME = 'jbrowse-msaview-blast-cache'\nconst STORE_NAME = 'blast-results'\nconst DB_VERSION = 2\n\n/**\n * How many results the history keeps. Every row holds a whole alignment and its\n * tree \u2014 megabytes each \u2014 so an unbounded store grows until the browser starts\n * refusing writes to it, and the user never sees why.\n */\nconst MAX_CACHED_RESULTS = 50\n\nexport interface CachedBlastResult {\n  id: string\n  proteinSequence: string\n  blastDatabase: BlastDatabase | PhmmerDatabase\n  /**\n   * Only ever set on rows cached by a version that still queried NCBI, where\n   * the choice between blastp and quick-blastp was real. Kept so those rows\n   * still display; never written now.\n   */\n  blastProgram?: string\n  /** absent on rows cached before phmmer existed, which were all blastp */\n  searchProgram?: SearchProgram\n  /** absent on phmmer rows, which are aligned by the search itself */\n  msaAlgorithm?: MsaAlgorithm\n  /** absent on rows saved before it was recorded */\n  maxHits?: number\n  msa: string\n  tree: string\n  treeMetadata: string\n  rid: string\n  timestamp: number\n  geneId?: string\n  transcriptId?: string\n  transcriptName?: string\n  geneName?: string\n}\n\ninterface BlastCacheDB extends DBSchema {\n  [STORE_NAME]: {\n    key: string\n    value: CachedBlastResult\n  }\n}\n\nconst getDB = createDbOpener<BlastCacheDB>(\n  DB_NAME,\n  DB_VERSION,\n  (db, oldVersion) => {\n    if (oldVersion < 2 && db.objectStoreNames.contains(STORE_NAME)) {\n      db.deleteObjectStore(STORE_NAME)\n    }\n    if (!db.objectStoreNames.contains(STORE_NAME)) {\n      db.createObjectStore(STORE_NAME, { keyPath: 'id' })\n    }\n  },\n)\n\n/**\n * One history row per distinct search. Every input that changes the stored\n * alignment is in the key, or re-running the query with another aligner or hit\n * count overwrites the earlier row. A part added later is left out at its old\n * value so rows saved before it still resolve: phmmer keys are prefixed and\n * blastp keys are not, and the hit count appears only when it is not the\n * default.\n */\nexport function createCacheKey({\n  proteinSequence,\n  blastDatabase,\n  msaAlgorithm,\n  searchProgram,\n  transcriptId,\n  maxHits,\n}: {\n  proteinSequence: string\n  blastDatabase: BlastDatabase | PhmmerDatabase\n  msaAlgorithm?: MsaAlgorithm\n  searchProgram?: SearchProgram\n  transcriptId?: string\n  maxHits?: number\n}) {\n  const idPart = transcriptId ? `:${transcriptId}` : ''\n  const hitsPart =\n    maxHits === undefined || maxHits === defaultMaxHits ? '' : `:n${maxHits}`\n  return searchProgram === 'phmmer'\n    ? `phmmer:${blastDatabase}${idPart}${hitsPart}:${proteinSequence}`\n    : `${blastDatabase}:${msaAlgorithm}${idPart}${hitsPart}:${proteinSequence}`\n}\n\n/**\n * Record a finished search in the history. Best effort: the alignment is\n * already in hand, and a browser refusing the write must not turn it into a\n * failed launch.\n */\nexport function saveBlastResult({\n  proteinSequence,\n  blastDatabase,\n  msaAlgorithm,\n  searchProgram,\n  maxHits,\n  msa,\n  tree,\n  treeMetadata,\n  rid,\n  geneId,\n  transcriptId,\n  transcriptName,\n  geneName,\n}: {\n  proteinSequence: string\n  blastDatabase: BlastDatabase | PhmmerDatabase\n  msaAlgorithm?: MsaAlgorithm\n  searchProgram?: SearchProgram\n  maxHits?: number\n  msa: string\n  tree: string\n  treeMetadata: string\n  rid: string\n  geneId?: string\n  transcriptId?: string\n  transcriptName?: string\n  geneName?: string\n}) {\n  return bestEffort(\n    'BLAST history write',\n    async () => {\n      const db = await getDB()\n      const entry: CachedBlastResult = {\n        id: createCacheKey({\n          proteinSequence,\n          blastDatabase,\n          msaAlgorithm,\n          searchProgram,\n          transcriptId,\n          maxHits,\n        }),\n        proteinSequence,\n        blastDatabase,\n        msaAlgorithm,\n        searchProgram,\n        maxHits,\n        msa,\n        tree,\n        treeMetadata,\n        rid,\n        timestamp: Date.now(),\n        geneId,\n        transcriptId,\n        transcriptName,\n        geneName,\n      }\n      await db.put(STORE_NAME, entry)\n      await evictOldest(db)\n      return entry\n    },\n    undefined,\n  )\n}\n\n/**\n * Drop the oldest rows until the store is back at MAX_CACHED_RESULTS.\n *\n * `count` first so the common save reads no values at all: without a timestamp\n * index the oldest have to be found by loading every row, and each one is an\n * entire alignment. Failing to evict must not fail the save \u2014 the result is\n * already in hand and losing it to a housekeeping error would be the worse\n * outcome.\n */\nasync function evictOldest(db: IDBPDatabase<BlastCacheDB>) {\n  try {\n    if ((await db.count(STORE_NAME)) <= MAX_CACHED_RESULTS) {\n      return\n    }\n    const all = await db.getAll(STORE_NAME)\n    const doomed = all\n      .toSorted((a, b) => a.timestamp - b.timestamp)\n      .slice(0, all.length - MAX_CACHED_RESULTS)\n    const tx = db.transaction(STORE_NAME, 'readwrite')\n    await Promise.all([...doomed.map(e => tx.store.delete(e.id)), tx.done])\n  } catch (e) {\n    console.warn('Failed to evict old BLAST cache entries:', e)\n  }\n}\n\nexport async function getAllCachedResults() {\n  const db = await getDB()\n  const results = await db.getAll(STORE_NAME)\n  return results.toSorted((a, b) => b.timestamp - a.timestamp)\n}\n\nexport async function deleteCachedResult(id: string) {\n  const db = await getDB()\n  await db.delete(STORE_NAME, id)\n}\n", "import { decodeXmlEntities, efetchUrl, eutilsText } from './eutils'\nimport { isAbortError } from './fetch'\nimport { bestEffort, createDbOpener } from './idb'\n\nimport type { DBSchema } from 'idb'\n\nconst DB_NAME = 'jbrowse-msaview-taxonomy-cache'\nconst STORE_NAME = 'common-names'\nconst DB_VERSION = 2\n\ninterface CachedTaxonomy {\n  taxid: number\n  sciname: string\n  commonName?: string\n}\n\ninterface TaxonomyCacheDB extends DBSchema {\n  [STORE_NAME]: {\n    key: number\n    value: CachedTaxonomy\n  }\n}\n\nconst getDB = createDbOpener<TaxonomyCacheDB>(DB_NAME, DB_VERSION, db => {\n  if (db.objectStoreNames.contains(STORE_NAME)) {\n    db.deleteObjectStore(STORE_NAME)\n  }\n  db.createObjectStore(STORE_NAME, { keyPath: 'taxid' })\n})\n\nfunction getCachedTaxonomies(taxids: number[]) {\n  return bestEffort(\n    'taxonomy cache read',\n    async () => {\n      const db = await getDB()\n      const tx = db.transaction(STORE_NAME, 'readonly')\n      const results = await Promise.all(\n        taxids.map(taxid => tx.store.get(taxid)),\n      )\n      await tx.done\n      return results\n    },\n    [],\n  )\n}\n\nfunction saveTaxonomyCache(entries: CachedTaxonomy[]) {\n  return bestEffort(\n    'taxonomy cache write',\n    async () => {\n      const db = await getDB()\n      const tx = db.transaction(STORE_NAME, 'readwrite')\n      for (const entry of entries) {\n        await tx.store.put(entry)\n      }\n      await tx.done\n    },\n    undefined,\n  )\n}\n\nexport interface TaxonomyInfo {\n  sciname: string\n  commonName?: string\n}\n\n/**\n * Names are a nicety, so a batch NCBI refuses leaves its taxa out of the\n * result rather than failing the caller. `onFailure` hears about each one, for\n * a caller that wants to say the names are missing.\n */\nexport async function fetchTaxonomyInfo(\n  taxidsWithRepeats: number[],\n  signal?: AbortSignal,\n  onFailure?: (error: unknown) => void,\n): Promise<Map<number, TaxonomyInfo>> {\n  // callers pass one taxid per alignment row, and a BLAST hit list is several\n  // rows per species: 100 albumin hits are maybe 50 taxa, and asking as they\n  // came did 100 IndexedDB reads and sent eutils 100 ids for 50 answers. The\n  // result is keyed by taxid, so no caller can tell the difference\n  const taxids = [...new Set(taxidsWithRepeats)]\n  const result = new Map<number, TaxonomyInfo>()\n  const uncachedTaxids: number[] = []\n  const cachedResults = await getCachedTaxonomies(taxids)\n\n  for (let i = 0; i < taxids.length; i++) {\n    const taxid = taxids[i]!\n    const cached = cachedResults[i]\n    if (cached) {\n      result.set(taxid, {\n        sciname: cached.sciname,\n        commonName: cached.commonName,\n      })\n    } else {\n      uncachedTaxids.push(taxid)\n    }\n  }\n\n  if (uncachedTaxids.length === 0) {\n    return result\n  }\n\n  const batchSize = 100\n  const toCache: CachedTaxonomy[] = []\n\n  for (let i = 0; i < uncachedTaxids.length; i += batchSize) {\n    const batch = uncachedTaxids.slice(i, i + batchSize)\n    const idsParam = batch.join(',')\n\n    try {\n      // textfetch rather than a bare fetch: an NCBI 429/5xx returns an HTML\n      // error body that the regexes below silently find nothing in, so without\n      // the status check a throttled batch looks like \"these taxa have no\n      // names\" instead of reporting why\n      const text = await eutilsText(\n        efetchUrl({ db: 'taxonomy', id: idsParam, retmode: 'xml' }),\n        { signal },\n      )\n\n      // Build a map of taxid -> taxon block by finding Taxon elements.\n      // Prefer entries with <LineageEx> (full top-level entries) over nested\n      // entries inside another taxon's LineageEx\n      const taxonMap = new Map<number, string>()\n      const taxonRegex = /<Taxon>\\s*<TaxId>(\\d+)<\\/TaxId>/g\n      let match\n      while ((match = taxonRegex.exec(text)) !== null) {\n        const matchedTaxid = Number(match[1])\n        const startIdx = match.index\n\n        // Find the matching closing </Taxon> by counting nesting depth\n        let depth = 1\n        let endIdx = startIdx + match[0].length\n        while (depth > 0 && endIdx < text.length) {\n          const openMatch = text.indexOf('<Taxon>', endIdx)\n          const closeMatch = text.indexOf('</Taxon>', endIdx)\n          if (closeMatch === -1) {\n            break\n          }\n          if (openMatch !== -1 && openMatch < closeMatch) {\n            depth++\n            endIdx = openMatch + 7\n          } else {\n            depth--\n            endIdx = closeMatch + 8\n          }\n        }\n\n        const taxonXml = text.slice(startIdx, endIdx)\n        const existing = taxonMap.get(matchedTaxid)\n        const hasLineageEx = taxonXml.includes('<LineageEx>')\n        const existingHasLineageEx = existing?.includes('<LineageEx>')\n        if (!existing || (hasLineageEx && !existingHasLineageEx)) {\n          taxonMap.set(matchedTaxid, taxonXml)\n        }\n      }\n\n      for (const taxid of batch) {\n        const taxonXml = taxonMap.get(taxid)\n        if (taxonXml) {\n          const genbankCommon =\n            /<GenbankCommonName>(.*?)<\\/GenbankCommonName>/.exec(taxonXml)\n          const commonName = /<CommonName>(.*?)<\\/CommonName>/.exec(taxonXml)\n          const sciName = /<ScientificName>(.*?)<\\/ScientificName>/.exec(\n            taxonXml,\n          )\n          const rawName = genbankCommon?.[1] ?? commonName?.[1]\n          const name = rawName && decodeXmlEntities(rawName)\n\n          const sci = decodeXmlEntities(sciName?.[1] ?? '')\n          result.set(taxid, { sciname: sci, commonName: name })\n          toCache.push({ taxid, sciname: sci, commonName: name })\n        }\n      }\n    } catch (error) {\n      if (isAbortError(error)) {\n        await saveTaxonomyCache(toCache)\n        throw error\n      }\n      console.error('Failed to fetch taxonomy data:', error)\n      onFailure?.(error)\n    }\n  }\n\n  if (toCache.length > 0) {\n    await saveTaxonomyCache(toCache)\n  }\n\n  return result\n}\n"],
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 }

package/dist/chunks/model-SEEQQSQO.js

@@ -0,0 +1,12 @@
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Try the BLAST tab, which needs no gene identifier.`);s(`Finding the UniRef${e} cluster of ${a.id}...`);let g=await or(a.accession,e,c);if(!g)throw new Error(`${a.accession} is in no UniRef${e} cluster`);let{total:C,scanned:Q,truncated:I,rows:d}=await ar({clusterId:g.id,identity:e,referenceProteomesOnly:n,taxa:r,exclude:o,limit:i,onProgress:s,signal:c});if(d.length<1)throw new Error(`${g.id} has no other ${n?"reference-proteome ":""}member to align ${a.id} against`);let h=rA(d.map(u=>u.commonName??u.scientificName));return{query:a,clusterId:g.id,total:C,warning:I?`${g.id} lists ${C??"more than "+Q} UniProtKB entries and the first ${Q} were read, so species whose only entries come later are missing.`:void 0,rows:d.map((u,l)=>({taxId:u.taxId,label:h[l],scientificName:u.scientificName,commonName:u.commonName,geneId:u.id,protein:u.accession,sequence:u.sequence}))}}async function sr(A,t){let e=A.blastParams;if(e.proteinSequence)return{sequence:GA(e.proteinSequence),name:A.querySeqName};if(e.accession){t.onProgress(`Fetching ${e.accession} from UniProt...`);let n=await ge([e.accession],0,t.signal);if(!n)throw new Error(`UniProt has no entry ${e.accession}`);let r=`${n.id}_query`;return t.act(()=>{A.setQuerySeqName(r)}),{sequence:n.sequence,name:r}}throw new Error("No query: a search needs a proteinSequence, a UniProt accession, or a connectedTranscript to translate")}async function gr({self:A,scope:t,query:e,querySeqName:n,maxHits:r,key:o}){let i=A.blastParams,{onProgress:s,onRid:c,signal:a}=t,{hits:g,queryRow:C,rid:Q}=await Bt[i.searchProgram??"blastp"]({query:e,database:i.blastDatabase,maxHits:r,onProgress:s,onRid:c,signal:a});if(g.length===0)throw new Error("No hits found");s("Fetching species taxonomy info...");let I=[],d=await iA(g.map(p=>p.taxid).filter(p=>p!==void 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n){o??=yt(i.gene);let s=yt(i.target_gene);s&&(i.ortholog==="LDO"||i.ortholog==="O")&&r.push({...s,symbol:i.target_gene_symbol===void 0?void 0:String(i.target_gene_symbol),type:i.ortholog})}return{unmapped:!!t?.unmapped_ids,query:o,hits:r}}function Br(A){let t=new Map;for(let e of A){let n=t.get(e.code);(!n||n.type==="O"&&e.type==="LDO")&&t.set(e.code,e)}return[...t.values()]}function Cr(A){let t=new Map;for(let e of A.results??[])e.primaryAccession&&e.sequence?.value&&t.set(e.primaryAccession,e.sequence.value);return t}var ce;function Er(){return ce??=O(`${kt}/supportedgenomes`).then(Ir).catch(A=>{throw ce=void 0,A}),ce}var Nt=100;async function dr(A,t){let e=new Map;for(let n=0;n<A.length;n+=Nt){let r=A.slice(n,n+Nt),o=await O(`${cr}/accessions?accessions=${r.join(",")}&fields=accession,sequence&format=json`,{signal:t});for(let[i,s]of Cr(o))e.set(i,s)}return e}async function fr(A,t,e,n){let r;for(let o of A){let i=JA(o);if(!i)continue;let s=new URLSearchParams({geneInputList:i,organism:String(t),orthologType:"all"});e&&s.set("targetOrganism",e.map(a=>a.taxId).join(","));let c=Qr(await O(`${kt}/ortholog/matchortho?${s.toString()}`,{signal:n}));if(!c.unmapped&&(r??=i,c.query))return{...c,matched:i}}return r===void 0?void 0:{matched:r,hits:[],query:void 0}}async function bt({candidates:A,taxId:t,taxa:e,exclude:n,limit:r=mA,onProgress:o,signal:i}){let s=await Er();i?.throwIfAborted();let c=new Map(s.map(E=>[E.taxId,E])),a=new Map(s.map(E=>[E.code,E])),g=c.get(t);if(!g)throw new Error(`PANTHER has no reference proteome for taxon ${t}. 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C=`${o}-${g}`;return{uniqueId:C,refName:a[0].refName,start:Math.min(...a.map(Q=>Q.start)),end:Math.max(...a.map(Q=>Q.end)),...i,type:"protein_domain",name:s,accession:c,subfeatures:a.map((Q,I)=>({uniqueId:`${C}-${I}`,refName:Q.refName,start:Q.start,end:Q.end,...i,type:"protein_domain_part"}))}})},displays:[{type:"LinearBasicDisplay",displayId:`${o}-LinearBasicDisplay`,color:{...r.color,title:"Domains"}}]}}var Jo=F(Yo()),qe=F(uA()),vo=F(Po()),Lo=F(ne()),Ae=F(vA());function Ro(A){return A.replace(/\.\d+$/,"")}function Ti(A,t){let e=Ro(t);return[A.get("name"),A.get("id"),A.get("transcript_id"),A.id()].some(n=>typeof n=="string"&&(n===t||Ro(n)===e))}function Go(A){return A.map(t=>({assemblyName:t.assemblyName,refName:t.refName,start:Math.floor(t.start),end:Math.ceil(t.end)}))}function Oi(A){let t=Go(A.dynamicBlocks?.contentBlocks??[]),e=Go(A.displayedRegions);return t.length>0?[t,e]:[e]}function Uo(A){return A.filter(t=>t.type==="FeatureTrack")}async function Zi(A,t){let e=A.connectedView,n=(0,qe.getSession)(A),r="msaview-connectedTranscript",o=Uo(e.tracks);for(let i of Oi(e))for(let s of o){let c=await n.rpcManager.call(r,"CoreGetFeatures",{adapterConfig:(0,Jo.getConf)(s,"adapter"),regions:i});for(let a of c){let g=Ze(a).find(C=>Ti(C,t));if(g)return g}}}async function Xi(A,t){let e=await Xe({start:t.get("start"),end:t.get("end"),refName:t.get("refName"),assemblyName:A.connectedView.assemblyNames[0],session:(0,qe.getSession)(A)});return(0,vo.translateTranscript)({transcript:t,...e})?.protein}var Ue=new WeakMap;async function Vi({self:A,transcriptId:t,blastParams:e,orthologParams:n,isCurrent:r}){let o=Uo(A.connectedView.tracks).length;try{A.setProgress(`Looking up ${t} in the genome view...`);let i=await Zi(A,t);if(!i)throw new Error(`Transcript "${t}" was not found in the ${o} feature track(s) open in the connected genome view. Open the gene track that carries it, and make sure the view is on its locus.`);let s=await Xi(A,i);if(!s)throw new Error(`Transcript "${t}" has no CDS to translate`);if(!r())return;let c=i.toJSON();(0,Ae.transaction)(()=>{A.setProgress(""),e&&!e.proteinSequence&&A.setBlastParams({...e,selectedTranscript:c,proteinSequence:s}),n&&!n.proteinSequence&&A.setOrthologParams({...n,selectedTranscript:c,proteinSequence:s}),A.setConnectedFeature(c)})}catch(i){console.error(i),r()&&(A.setProgress(""),A.setError(i))}}function qo(A){let{connectedTranscript:t,connectedFeature:e,connectedView:n,blastParams:r,orthologParams:o}=A;if(!t||e||!n?.initialized||n.tracks.length===0)return;let i=(Ue.get(A)??0)+1;Ue.set(A,i),(0,Ae.untracked)(()=>{Vi({self:A,transcriptId:t,blastParams:r,orthologParams:o,isCurrent:()=>(0,Lo.isAlive)(A)&&Ue.get(A)===i})})}var ug=["ncbi","panther","uniref"];function ji(){return b.types.compose(_o.BaseViewModel,ot(),b.types.model("MsaView",{connectedViewId:b.types.maybe(b.types.string),connectedFeature:b.types.frozen(),connectedTranscript:b.types.maybe(b.types.string),blastParams:b.types.frozen(),orthologParams:b.types.frozen(),querySeqName:b.types.stripDefault(b.types.string,"QUERY"),querySeqOffset:b.types.stripDefault(b.types.number,0),uniprotId:b.types.maybe(b.types.string),zoomToBaseLevel:b.types.stripDefault(b.types.boolean,!1),init:b.types.frozen(),dataStoreId:b.types.maybe(b.types.string),launchCompleted:!1,mafRegion:b.types.frozen(),embeddedMode:!0,domainsOnGenome:b.types.stripDefault(b.types.boolean,!1)})).volatile(()=>({rid:void 0,progress:"",loadingStoredData:!1,isStoringData:!1,lastStoredData:void 0,ownsDataStoreRow:!1,launchController:void 0,domainsRequested:!1})).views(A=>({get transcriptToMsaMap(){return A.connectedFeature?Io(A.connectedFeature):void 0},get connectedView(){let{views:t}=(0,K.getSession)(A);return t.find(e=>e.id===A.connectedViewId)}})).views(A=>({get connectedHoverHighlights(){let{mouseCol:t}=A;return t===void 0?[]:$A({model:A,coord:t})},get connectedClickHighlights(){let{mouseClickCol:t}=A;return t===void 0?[]:$A({model:A,coord:t})},get connectedHighlights(){return[...this.connectedHoverHighlights,...this.connectedClickHighlights]},get connectedDomains(){return xo(A)}})).views(A=>({get hostRestoresData(){let{msaIndexedLocation:t,msaName:e}=A.init??{};return A.hostCarriesData||!!(t&&e)},get unsavedDocuments(){let{data:t,init:e}=A,n=(0,b.getSnapshot)(t),r=(o,i)=>{let s=t[o];return s&&!i&&!n[o]?s:void 0};return{msa:r("msa",A.msaFilehandle??e?.msaIndexedLocation),tree:r("tree",A.treeFilehandle),treeMetadata:r("treeMetadata",A.treeMetadataFilehandle),gff:r("gff",A.gffFilehandle)}}})).actions(A=>({setZoomToBaseLevel(t){A.zoomToBaseLevel=t},setProgress(t){A.progress=t},setRid(t){A.rid=t},setBlastParams(t){A.blastParams=t},setConnectedFeature(t){A.connectedFeature=t},setOrthologParams(t){A.orthologParams=t},setInit(t){A.init=t},setQuerySeqName(t){A.querySeqName=t},setUniprotId(t){A.uniprotId=t},setDataStoreId(t){A.dataStoreId=t},setLaunchCompleted(t){A.launchCompleted=t},setLoadingStoredData(t){A.loadingStoredData=t},setIsStoringData(t){A.isStoringData=t},setLastStoredData(t){A.lastStoredData=t},setOwnsDataStoreRow(t){A.ownsDataStoreRow=t},setLaunchController(t){A.launchController=t},cancelLaunch(){A.launchController?.abort(),A.launchController=void 0,A.blastParams=void 0,A.orthologParams=void 0,A.init=void 0,A.launchCompleted=!1,A.progress="",A.rid=void 0,A.error=void 0},retryLaunch(){A.launchController?.abort(),A.launchController=void 0,A.progress="",A.rid=void 0,A.error=void 0,A.launchCompleted=!1,A.blastParams&&(A.blastParams={...A.blastParams}),A.orthologParams&&(A.orthologParams={...A.orthologParams}),A.init&&(A.init={...A.init})},setDomainsRequested(t){A.domainsRequested=t},setDomainsOnGenome(t){A.domainsOnGenome=t},showDomainsOnGenome(){let t=(0,K.getSession)(A),{connectedView:e,connectedDomains:n,connectedFeature:r}=A,o=e?.assemblyNames[0];if(!e||!o||n.features.length===0||!(0,K.isSessionWithAddSessionTrack)(t))return;let i=r,s=[i?.gene_name,i?.gene,i?.name].find(g=>typeof g=="string"&&g!==""),c=Fo({viewId:A.id,assemblyName:o,name:`${s??A.querySeqName} domains (from the alignment)`,strand:A.mafRegion?void 0:A.transcriptToMsaMap?.strand,domains:n}),a=(0,K.isSessionWithSessionTracks)(t)?t.sessionTracks.find(g=>g.trackId===c.trackId):void 0;a&&(0,K.isSessionWithDeleteTrackConf)(t)&&t.deleteTrackConf(a),t.addSessionTrackConf(c)&&e.launchTrack(c.trackId)},handleMsaClick(t){let{connectedView:e,zoomToBaseLevel:n}=A,r=Mo({model:A,coord:t});!r||!e||(n?e.navTo(r):e.centerAt(r.start,r.refName))}})).actions(A=>{let t=A.setMouseClickPos.bind(A);return{setMouseClickPos(e,n){t(e,n),e!==void 0&&A.handleMsaClick(e)}}}).actions(A=>{let t=A.reset.bind(A);return{reset(){let{displayName:e,minimized:n,zoomToBaseLevel:r}=A;t(),e!==void 0&&A.setDisplayName(e),A.setMinimized(n),A.setZoomToBaseLevel(r),A.setDomainsRequested(!1),A.setLastStoredData(void 0),A.setOwnsDataStoreRow(!1)}}}).views(A=>{let t=A.menuItems.bind(A);return{menuItems(){return[...t(),{label:"Zoom to base level on click?",type:"checkbox",checked:A.zoomToBaseLevel,onClick:()=>{A.setZoomToBaseLevel(!A.zoomToBaseLevel)}},...A.connectedView&&A.connectedDomains.features.length>0?[{label:"Show domains on the genome",onClick:()=>{A.showDomainsOnGenome()}}]:[]]}}}).actions(A=>({afterCreate(){bo(),(0,b.addDisposer)(A,()=>{A.launchController?.abort()}),lo(A);for(let t of[mo,qo,po,wo,yo,Do,So])(0,b.addDisposer)(A,(0,ee.autorun)(()=>{t(A)}));(0,b.addDisposer)(A,(0,ee.autorun)(No(A))),(0,b.addDisposer)(A,(0,ee.autorun)(ko(A)))}}))}export{ji as default,ug as orthologSources};
+//# sourceMappingURL=model-SEEQQSQO.js.map