jbrowse-plugin-msaview 4.0.0 → 5.1.0

package/dist/chunks/{LaunchMsaViewDialog-54LBEZHK.js → LaunchMsaViewDialog-WBXEEHJL.js}

@@ -1,5 +1,5 @@
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-//# sourceMappingURL=LaunchMsaViewDialog-54LBEZHK.js.map
+//# sourceMappingURL=LaunchMsaViewDialog-WBXEEHJL.js.map

package/dist/chunks/chunk-DECSTFAT.js

@@ -0,0 +1,2 @@
+var w=["stack","splitRight","newTab"],i="splitRight",r="msaView-launchPlacement";function o(e,t){return t in e&&typeof e[t]=="function"}var a=!1;function M(e){return c(e)||o(e,"setUseWorkspaces")&&o(e,"setPendingMove")}function c(e){return o(e,"moveViewToNewTab")&&o(e,"moveViewToSplit")}function p(e){let t=o(e,"setUseWorkspaces"),s=o(e,"setPendingMove");return t!==s&&!a&&(a=!0,console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ${s?"setUseWorkspaces":"setPendingMove"}, so the MSA view was stacked instead of tiled: the session API moved and the plugin needs updating to match.`)),t&&s}function l(e,t,s){s!=="stack"&&(c(e)?s==="newTab"?e.moveViewToNewTab(t):e.moveViewToSplit(t,"row"):p(e)&&(e.setPendingMove({type:s,viewId:t}),e.setUseWorkspaces(!0)))}function u(e){return w.includes(e)}function m(){try{let e=globalThis.localStorage.getItem(r);return u(e)?e:i}catch(e){return console.error(e),i}}function d(e){try{globalThis.localStorage.setItem(r,e)}catch(t){console.error(t)}}async function P(e,{placement:t="stack",...s}){let n=await e.launchView("MsaView",{type:"MsaView",...s});return l(e,n.id,t),n}export{M as a,m as b,d as c,P as d};
+//# sourceMappingURL=chunk-DECSTFAT.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/workspaces.ts", "../../src/utils/launchMsaView.ts"],
+  "sourcesContent": ["import type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * Where a launched MSA view lands. Every launch names one of these and stops\n * there, so a host that arranges views differently is one function to teach.\n *\n *   stack       append below whatever is on screen\n *   splitRight  its own cell to the right, beside the view it is connected to\n *   newTab      its own tab in the current cell\n */\nexport type MsaViewPlacement = 'stack' | 'splitRight' | 'newTab'\n\nconst PLACEMENTS: MsaViewPlacement[] = ['stack', 'splitRight', 'newTab']\n\n/**\n * What the dialog does unasked. Side-by-side, because a launch from a gene\n * feature sets `connectedViewId`: the pair shares a hover and a highlight, and\n * reads as a split. A session spec defaults to `stack` instead.\n */\nexport const DEFAULT_LAUNCH_PLACEMENT: MsaViewPlacement = 'splitRight'\n\nexport const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement'\n\n/**\n * The session actions that place a view in a tiled workspace. Only jbrowse-web\n * and desktop have them, so feature-detect rather than import.\n */\ninterface SessionWithMoves {\n  moveViewToNewTab: (viewId: string) => unknown\n  moveViewToSplit: (viewId: string, direction: 'row' | 'column') => unknown\n}\n\n// a host from before the workspace was always on\ninterface SessionWithWorkspaces {\n  setUseWorkspaces: (useWorkspaces: boolean) => void\n  setPendingMove: (move: {\n    type: 'newTab' | 'splitRight'\n    viewId: string\n  }) => void\n}\n\nfunction hasAction(session: AbstractSessionModel, name: string) {\n  return (\n    name in session &&\n    typeof (session as unknown as Record<string, unknown>)[name] === 'function'\n  )\n}\n\n// Warned at most once. This is a property of the host, so the answer is the\n// same on every launch and a dialog the user reopens should not stack up noise.\nlet warnedPartial = false\n\nexport function resetWorkspacesWarning() {\n  warnedPartial = false\n}\n\n/**\n * Whether this host can honor anything other than `stack`. Silent: the dialog\n * asks on every render, and only a launch is worth warning about.\n */\nexport function sessionSupportsPlacement(session: AbstractSessionModel) {\n  return (\n    isSessionWithMoves(session) ||\n    (hasAction(session, 'setUseWorkspaces') &&\n      hasAction(session, 'setPendingMove'))\n  )\n}\n\nfunction isSessionWithMoves(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithMoves {\n  return (\n    hasAction(session, 'moveViewToNewTab') &&\n    hasAction(session, 'moveViewToSplit')\n  )\n}\n\nfunction isSessionWithWorkspaces(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithWorkspaces {\n  const canEnable = hasAction(session, 'setUseWorkspaces')\n  const canPlace = hasAction(session, 'setPendingMove')\n\n  // Missing BOTH is an embedded session, with nothing to ask for. Missing ONE\n  // is a host that moved the action out from under us: protein3d once stopped\n  // tiling silently for weeks when jbrowse-web folded `setPendingMove` into its\n  // layout `init`.\n  if (canEnable !== canPlace && !warnedPartial) {\n    warnedPartial = true\n    console.warn(\n      `jbrowse-plugin-msaview: this session supports workspaces but not ` +\n        `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the MSA view ` +\n        `was stacked instead of tiled: the session API moved and the plugin ` +\n        `needs updating to match.`,\n    )\n  }\n  return canEnable && canPlace\n}\n\n/**\n * Put a freshly added view where the launch said to. `stack` is a placement\n * rather than the absence of one, so no caller has to ask what host it is on.\n */\nexport function placeMsaView(\n  session: AbstractSessionModel,\n  viewId: string,\n  placement: MsaViewPlacement,\n) {\n  if (placement === 'stack') {\n    return\n  }\n  if (isSessionWithMoves(session)) {\n    if (placement === 'newTab') {\n      session.moveViewToNewTab(viewId)\n    } else {\n      session.moveViewToSplit(viewId, 'row')\n    }\n  } else if (isSessionWithWorkspaces(session)) {\n    session.setPendingMove({ type: placement, viewId })\n    session.setUseWorkspaces(true)\n  }\n}\n\nfunction isPlacement(value: unknown): value is MsaViewPlacement {\n  return PLACEMENTS.includes(value as MsaViewPlacement)\n}\n\n/**\n * The dialog's own remembered choice \u2014 not the host's preferences system, which\n * records whether the user likes workspaces and does not exist everywhere.\n */\nexport function readLaunchPlacement(): MsaViewPlacement {\n  try {\n    const stored = globalThis.localStorage.getItem(LAUNCH_PLACEMENT_KEY)\n    return isPlacement(stored) ? stored : DEFAULT_LAUNCH_PLACEMENT\n  } catch (error) {\n    console.error(error)\n    return DEFAULT_LAUNCH_PLACEMENT\n  }\n}\n\nexport function writeLaunchPlacement(placement: MsaViewPlacement) {\n  try {\n    globalThis.localStorage.setItem(LAUNCH_PLACEMENT_KEY, placement)\n  } catch (error) {\n    console.error(error)\n  }\n}\n", "import { placeMsaView } from './workspaces'\n\nimport type { MsaViewPlacement } from './workspaces'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * A launch, stated: what the view is, and where it goes. Everything but\n * `placement` is a react-msaview or plugin-model snapshot property, passed\n * through untouched so this never becomes a list that has to grow.\n */\nexport interface MsaViewLaunchSpec extends Record<string, unknown> {\n  /** default `stack`, the only thing an embedded session can do */\n  placement?: MsaViewPlacement\n}\n\n/**\n * The one place a launch adds an MSA view -- the dialog's four tabs, the Add\n * menu, and the `LaunchView-MsaView` extension point a session spec arrives on\n * all come through here. Each of them used to run its own `addView` and none\n * placed the result, which is how a launch from a gene feature landed stacked\n * under the very genome view it was connected to.\n */\nexport async function launchMsaView(\n  session: AbstractSessionModel,\n  { placement = 'stack', ...snapshot }: MsaViewLaunchSpec,\n) {\n  const view = await session.launchView('MsaView', {\n    type: 'MsaView',\n    ...snapshot,\n  })\n  placeMsaView(session, view.id, placement)\n  return view\n}\n"],
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+}

package/dist/chunks/chunk-MHBTV7BZ.js

@@ -0,0 +1,3 @@
+import{b as X,c as I,d as K,e as H,o as J}from"./chunk-PJZ3XTMG.js";import{a as Pe}from"./chunk-IBBQUV2I.js";import{a as Te}from"./chunk-2IWD4OO4.js";import{a as Be,b as z}from"./chunk-FY3BTKY4.js";var Ae=Be((gt,te)=>{te.exports=JBrowseExports["@jbrowse/core/util/translateTranscript"]});var E=z(Pe());function ot(e){return(0,E.getContainingView)(e)}function Z(e){return typeof e=="string"&&e!==""}function Y(e){return[...new Set(e.filter(Z))]}function ee(e,t){return t.filter(Z).join(e)}function Ce(e){let n=(e.get("subfeatures")??[]).filter(r=>(r.get("type")==="mRNA"||r.get("type")==="transcript")&&r.get("subfeatures")?.some(o=>o.get("type")==="CDS"));return n.length>0?n:[e]}function Q(e){let t=(0,E.sum)(e.get("subfeatures")?.filter(n=>n.get("type")==="CDS").map(n=>n.get("end")-n.get("start"))??[]);return{len:Math.floor(t/3),mod:t%3}}function st(e){return e?.id()??""}function Ne(e){return e?Y([e.id(),e.get("name"),e.get("id"),e.get("transcript_id")]):[]}function it(e,t){return Ne(e).includes(t)}function Ee(e){return e?ee(" ",[e.get("name"),e.get("id")]):""}function Me(e){return e?ee(" ",[e.get("gene_name")??e.get("name"),e.get("id")?`(${e.get("id")})`:void 0]):""}function at(e,t){return`BLAST - ${Me(e)} - ${Ee(t)}`}function ct(e){return Ce(e).toSorted((n,r)=>Q(r).len-Q(n).len)}function ut(e){return e.replace(/[*&]+$/,"").replaceAll(/[*&]/g,"X")}function mt(e){return Y([e.id(),e.get("id"),e.get("name"),e.get("gene_id"),e.get("gene_name")])}var ne=z(Te());async function lt({start:e,end:t,refName:n,session:r,assemblyName:o}){let{assemblyManager:a,rpcManager:i}=r,c=await a.waitForAssembly(o);if(!c)throw new Error("assembly not found");return{seq:(await i.call("getSequence","CoreGetFeatures",{adapterConfig:(0,ne.getConf)(c,["sequence","adapter"]),regions:[{start:e,end:t,refName:c.getCanonicalRefName(n)??n,assemblyName:o}]}))[0]?.get("seq")??"",assemblyGeneticCodeId:c.getGeneticCodeId(n)}}var _e="jbrowse-plugin-msaview",Re="colin.diesh@gmail.com",oe="https://eutils.ncbi.nlm.nih.gov/entrez/eutils";function se(e){return new URLSearchParams({...e,tool:_e,email:Re})}function L(e,t){return`${oe}/${e}.fcgi?${se(t).toString()}`}function A(e){return L("efetch",e)}function ie(e){return[`${oe}/efetch.fcgi`,{method:"POST",body:se(e)}]}var re=350,M=0;async function ae(e){let t=Date.now(),n=Math.max(t,M);if(M=n+re,n>t)try{await K(n-t,e??void 0)}catch(r){throw M===n+re&&(M=n),r}}async function S(e,t){return await ae(t?.signal),X(e,t)}async function ce(e,t){return await ae(t?.signal),I(e,t)}var Oe={amp:"&",apos:"'",gt:">",lt:"<",quot:'"'};function j(e){return e.replaceAll(/&(#x[\da-f]+|#\d+|[a-z]+);/gi,(t,n)=>n.startsWith("#x")||n.startsWith("#X")?String.fromCodePoint(Number.parseInt(n.slice(2),16)):n.startsWith("#")?String.fromCodePoint(Number(n.slice(1))):Oe[n]??t)}var me="https://api.ncbi.nlm.nih.gov/datasets/v2",$e=100;function Le(e){return e.trim().replace(/^\w+:/,"").replace(/\.\d+$/,"")}async function wt(e,t,n){let r=new Set;for(let o of e){let a=o.trim();if(/^\d+$/.test(a))return{geneId:a,matched:a};let i=Le(a);if(!i||r.has(i))continue;r.add(i);let s=(await ce(L("esearch",{db:"gene",term:`${i}[Gene Name] AND ${t}[taxid]`,retmode:"json",retmax:"1"}),{signal:n})).esearchresult?.idlist?.[0];if(s)return{geneId:s,matched:i}}}async function je(e,{taxa:t,exclude:n,limit:r=$e,signal:o}={}){let a=await I(`${me}/gene/id/${e}/orthologs?returned_content=COMPLETE`,{signal:o}),i=new Map;for(let{gene:c}of a.reports??[]){let s=Number(c?.tax_id);if(c?.gene_id&&s!==n&&(t?.has(s)??!0)&&!i.has(s)&&i.set(s,{taxId:s,geneId:c.gene_id,scientificName:c.taxname??String(s),commonName:c.common_name}),i.size>=r)break}return[...i.values()]}var ue=150;async function de(e,t){let n=new Map;for(let r=0;r<e.length;r+=ue){let o=e.slice(r,r+ue),a=await I(`${me}/gene/id/${o.join(",")}/product_report?page_size=${o.length}`,{signal:t});for(let{product:i}of a.reports??[]){let c=(i?.transcripts??[]).map(u=>({acc:u.protein?.accession_version,len:u.protein?.length??0,mane:/select/i.test(u.select_category??"")})).filter(u=>!!u.acc),s=c.find(u=>u.mane)??[...c].sort((u,d)=>d.len-u.len).at(0);i?.gene_id&&s&&n.set(i.gene_id,s.acc)}}return n}function ge(e){let t=new Map,n,r=[];for(let o of e.split(`
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0||a===J?"":`:n${a}`;return r==="phmmer"?`phmmer:${t}${i}${c}:${e}`:`${t}:${n}${i}${c}:${e}`}function Nt({proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,maxHits:o,msa:a,tree:i,treeMetadata:c,rid:s,geneId:u,transcriptId:d,transcriptName:g,geneName:x}){return B("BLAST history write",async()=>{let y=await W(),l={id:Ye({proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,transcriptId:d,maxHits:o}),proteinSequence:e,blastDatabase:t,msaAlgorithm:n,searchProgram:r,maxHits:o,msa:a,tree:i,treeMetadata:c,rid:s,timestamp:Date.now(),geneId:u,transcriptId:d,transcriptName:g,geneName:x};return await y.put(f,l),await et(y),l},void 0)}async function et(e){try{if(await e.count(f)<=De)return;let t=await e.getAll(f),n=t.toSorted((o,a)=>o.timestamp-a.timestamp).slice(0,t.length-De),r=e.transaction(f,"readwrite");await Promise.all([...n.map(o=>r.store.delete(o.id)),r.done])}catch(t){console.warn("Failed to evict old BLAST cache entries:",t)}}async function Et(){return(await(await W()).getAll(f)).toSorted((n,r)=>r.timestamp-n.timestamp)}async function Mt(e){await(await W()).delete(f,e)}var tt="jbrowse-msaview-taxonomy-cache",T="common-names",nt=2,Se=R(tt,nt,e=>{e.objectStoreNames.contains(T)&&e.deleteObjectStore(T),e.createObjectStore(T,{keyPath:"taxid"})});function rt(e){return B("taxonomy cache read",async()=>{let n=(await Se()).transaction(T,"readonly"),r=await Promise.all(e.map(o=>n.store.get(o)));return await n.done,r},[])}function Ie(e){return B("taxonomy cache write",async()=>{let n=(await Se()).transaction(T,"readwrite");for(let r of e)await n.store.put(r);await n.done},void 0)}async function $t(e,t){let n=[...new Set(e)],r=new Map,o=[],a=await rt(n);for(let s=0;s<n.length;s++){let u=n[s],d=a[s];d?r.set(u,{sciname:d.sciname,commonName:d.commonName}):o.push(u)}if(o.length===0)return r;let i=100,c=[];for(let s=0;s<o.length;s+=i){let u=o.slice(s,s+i),d=u.join(",");try{let g=await S(A({db:"taxonomy",id:d,retmode:"xml"}),{signal:t}),x=new Map,y=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,l;for(;(l=y.exec(g))!==null;){let m=Number(l[1]),h=l.index,p=1,b=h+l[0].length;for(;p>0&&b<g.length;){let O=g.indexOf("<Taxon>",b),$=g.indexOf("</Taxon>",b);if($===-1)break;O!==-1&&O<$?(p++,b=O+7):(p--,b=$+8)}let P=g.slice(h,b),D=x.get(m),C=P.includes("<LineageEx>"),N=D?.includes("<LineageEx>");(!D||C&&!N)&&x.set(m,P)}for(let m of u){let h=x.get(m);if(h){let p=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(h),b=/<CommonName>(.*?)<\/CommonName>/.exec(h),P=/<ScientificName>(.*?)<\/ScientificName>/.exec(h),D=p?.[1]??b?.[1],C=D&&j(D),N=j(P?.[1]??"");r.set(m,{sciname:N,commonName:C}),c.push({taxid:m,sciname:N,commonName:C})}}}catch(g){if(H(g))throw await Ie(c),g;console.error("Failed to fetch taxonomy data:",g)}}return c.length>0&&await Ie(c),r}export{ot as a,Ce as b,Q as c,st as d,it as e,Ee as f,Me as g,at as h,ct as i,ut as j,mt as k,Ae as l,lt as m,R as n,B as o,Nt as p,Et as q,Mt as r,L as s,A as t,S as u,ce as v,j as w,$e as x,Le as y,wt as z,ke as A,yt as B,Dt as C,$t as D};
+//# sourceMappingURL=chunk-MHBTV7BZ.js.map

package/dist/chunks/chunk-MHBTV7BZ.js.map

@@ -0,0 +1,7 @@
+{
+  "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@8.0.3/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 = 'colin.diesh@gmail.com'\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 { 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+$/, '')\n}\n\n/**\n * A free-text gene reference -> NCBI gene id. A bare number is taken as the id\n * itself; anything else is searched as a gene name within the query taxon.\n * Several candidate identifiers are tried in order, because a JBrowse feature\n * carries whatever its GFF/BigBed had \u2014 `id()`, `name`, `gene_name` \u2014 and only\n * some of those are real symbols. `gene:TP53` and `TP53` are one search.\n */\nexport async function resolveGeneId(\n  candidates: string[],\n  taxId: number,\n  signal?: AbortSignal,\n): Promise<{ geneId: string; matched: string } | undefined> {\n  const asked = new Set<string>()\n  for (const raw of candidates) {\n    const query = raw.trim()\n    if (/^\\d+$/.test(query)) {\n      return { geneId: query, matched: query }\n    }\n    const cleaned = cleanGeneCandidate(query)\n    if (!cleaned || asked.has(cleaned)) {\n      continue\n    }\n    asked.add(cleaned)\n    const json = await eutilsJson<{\n      esearchresult?: { idlist?: string[] }\n    }>(\n      eutilsUrl('esearch', {\n        db: 'gene',\n        term: `${cleaned}[Gene Name] AND ${taxId}[taxid]`,\n        retmode: 'json',\n        retmax: '1',\n      }),\n      { signal },\n    )\n    const geneId = json.esearchresult?.idlist?.[0]\n    if (geneId) {\n      return { geneId, matched: cleaned }\n    }\n  }\n  return undefined\n}\n\ninterface OrthologReport {\n  reports?: {\n    gene?: {\n      gene_id?: string\n      tax_id?: string | number\n      taxname?: string\n      common_name?: string\n    }\n  }[]\n}\n\n/**\n * One ortholog gene per species, in NCBI's report order, capped at `limit`.\n *\n * `taxa` narrows the set when a caller wants specific species; omitted, every\n * species NCBI has an ortholog for is a candidate. `exclude` drops the query\n * taxon, which already has its own `<species>_query` row.\n */\nexport async function fetchOrthologGenes(\n  geneId: string,\n  {\n    taxa,\n    exclude,\n    limit = defaultMaxSpecies,\n    signal,\n  }: {\n    taxa?: Set<number>\n    exclude?: number\n    limit?: number\n    signal?: AbortSignal\n  } = {},\n) {\n  const json = await jsonfetch<OrthologReport>(\n    `${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            IDBDatabase,\n            IDBObjectStore,\n            IDBIndex,\n            IDBCursor,\n            IDBTransaction,\n        ]));\n}\n// This is a function to prevent it throwing up in node environments.\nfunction getCursorAdvanceMethods() {\n    return (cursorAdvanceMethods ||\n        (cursorAdvanceMethods = [\n            IDBCursor.prototype.advance,\n            IDBCursor.prototype.continue,\n            IDBCursor.prototype.continuePrimaryKey,\n        ]));\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 (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 = new Map();\nfunction getMethod(target, prop) {\n    if (!(target instanceof IDBDatabase &&\n        !(prop in target) &&\n        typeof prop === 'string')) {\n        return;\n    }\n    if (cachedMethods.get(prop))\n        return cachedMethods.get(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    cachedMethods.set(prop, method);\n    return 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 = ['continue', 'continuePrimaryKey', 'advance'];\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\nexport async function fetchTaxonomyInfo(\n  taxidsWithRepeats: number[],\n  signal?: AbortSignal,\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    }\n  }\n\n  if (toCache.length > 0) {\n    await saveTaxonomyCache(toCache)\n  }\n\n  return result\n}\n"],
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+}