jbrowse-plugin-msaview 3.7.1 → 3.8.0

package/dist/LaunchMsaView/launchTarget.d.ts

@@ -6,6 +6,9 @@ export interface ContextMenuInfo {
         featureId: string;
         type?: string;
     };
+    subfeature?: {
+        featureId: string;
+    };
     displayedRegionIndex: number;
 }
 export interface DisplayModel {

package/dist/LaunchMsaView/launchTarget.js

@@ -38,6 +38,7 @@ export function launchTarget(self) {
         return isGeneLikeType(info.item.type)
             ? {
                 fetchFeature: () => fetchFullFeature(info.item.featureId, info.displayedRegionIndex),
+                preferredTranscriptId: info.subfeature?.featureId,
             }
             : undefined;
     }

package/dist/LaunchMsaView/launchTarget.test.js

@@ -108,6 +108,19 @@ describe('launchTarget', () => {
         // the choice is ever stated
         expect(target?.preferredTranscriptId).toBe(mrna.id());
     });
+    // the canvas host names the clicked isoform beside the gene it fetches, as
+    // its own Collapse introns dialog reads it
+    test('carries the isoform a canvas click landed on', () => {
+        const host = modernHost('gene');
+        const target = launchTarget({
+            ...host,
+            contextMenuInfo: {
+                ...host.contextMenuInfo,
+                subfeature: { featureId: 'mrna-2' },
+            },
+        });
+        expect(target?.preferredTranscriptId).toBe('mrna-2');
+    });
     // a host that has both shapes must not fall through to the legacy branch and
     // launch on a stale feature when the click was not on a gene
     test('a non-gene click on a host carrying both shapes offers nothing', () => {

package/dist/MsaViewPanel/model.d.ts

@@ -1016,10 +1016,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setQuerySeqName(arg: string): void;
-    /**
-     * #action
-     */
-    setQuerySeqOffset(arg: number): void;
     /**
      * #action
      */
@@ -1032,10 +1028,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setLaunchCompleted(arg: boolean): void;
-    /**
-     * #action
-     */
-    setMafRegion(arg?: MafRegion): void;
     /**
      * #action
      */

package/dist/MsaViewPanel/model.js

@@ -269,12 +269,6 @@ export default function stateModelFactory() {
         setQuerySeqName(arg) {
             self.querySeqName = arg;
         },
-        /**
-         * #action
-         */
-        setQuerySeqOffset(arg) {
-            self.querySeqOffset = arg;
-        },
         /**
          * #action
          */
@@ -293,12 +287,6 @@ export default function stateModelFactory() {
         setLaunchCompleted(arg) {
             self.launchCompleted = arg;
         },
-        /**
-         * #action
-         */
-        setMafRegion(arg) {
-            self.mafRegion = arg;
-        },
         /**
          * #action
          */

package/dist/jbrowse-plugin-msaview.umd.production.min.js

@@ -91,11 +91,11 @@ ${r??t}`,...a].join(`
 ${C}`,...b.map(v=>`>${v.label}
 ${v.sequence}`)].join(`
 `),onProgress:f,signal:d}),treeMetadata:JSON.stringify(x)}}async function ore({taxId:e,geneCandidates:t,onProgress:r,...n}){r("Resolving gene at NCBI...");let o=await b4(t,e);if(!o)throw new Error(`Could not resolve any of ${t.join(", ")} to an NCBI gene in taxon ${e}. Try the NCBI BLAST tab, which needs no gene identifier.`);let i=await lre(o.geneId),s=await w4({geneId:o.geneId,onProgress:r,...n});return{geneId:o.geneId,representative:i,rows:s}}var ire={ncbi:"NCBI",panther:"PANTHER",uniref:"UniProt"};async function sre({geneCandidates:e,identity:t,referenceProteomesOnly:r,signal:n,...o}){let i=await v4({candidates:e,identity:t,referenceProteomesOnly:r,signal:n,...o});return{geneId:i.query.id,representative:{accession:i.query.accession,sequence:i.query.sequence},rows:i.rows}}async function are({geneCandidates:e,...t}){let r=await _4({candidates:e,...t});return{geneId:r.query?.geneRef??r.matched,representative:r.query,rows:r.rows}}async function cre(e,t){let r;try{let n=(await ii([e])).get(e);r=n?.commonName??n?.sciname}catch(n){console.warn("[msaview-orthologs] taxonomy name lookup failed:",n)}return xs([...t.map(n=>n.label),`${r??"query"}_query`]).at(-1)}async function lre(e){try{return await E4(e)}catch(t){console.warn("[msaview-orthologs] query protein lookup failed:",t);return}}function ure(e,t,r,n){let o={"Gene ID":t},i=VA(e.orthologParams?.selectedTranscript);return i&&(o.Transcript=i),n?.sequence===r&&(o.Accession=n.accession),o}function fre(e){let t={"Scientific name":e.scientificName,Accession:e.protein,"Gene ID":e.geneId};return e.commonName&&(t["Common name"]=e.commonName),t}l6();var f6=g(CA());async function d6({location:e,name:t}){let r=i=>(0,f6.openLocation)({uri:i,locationType:"UriLocation"}),n=await r(`${e.uri}.idx`).readFile("utf8"),o=ene(n,t);if(o){let s=await new _c({filehandle:r(e.uri),gziFilehandle:r(`${e.uri}.gzi`)}).read(o.length,o.offset);return new TextDecoder().decode(s).trim()}}var u6=e=>e.replace(/\.\d+$/,"");function ene(e,t){let r=u6(t);for(let n of e.split(`
-`)){let[o,i,s]=n.split("	");if(o&&u6(o)===r)return{offset:Number(i),length:Number(s)}}}var m6=g(Ve());function p6({model:e}){let{assemblyManager:t,hovered:r}=(0,m6.getSession)(e),{transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Es(r)||!$A(e))return;let{coord:s,refName:a}=r.hoverPosition,l=s-1,c=t.get(i?.assemblyName??o.assemblyNames[0]??""),u=m=>(c?.initialized?c.getCanonicalRefName(m):void 0)??m,f=u(a);if(i)return f!==u(i.refName)||!o.assemblyNames.includes(i.assemblyName)||l<i.start||l>=i.end?void 0:_E(e,l-i.start);if(n&&f===u(n.refName)){let m=n.g2p[l];if(m!==void 0)return jA(e,m)}}var tne="jbrowse-msaview-domain-cache",ig="domains",rne=1,A6=ni(tne,rne,e=>{e.objectStoreNames.contains(ig)||e.createObjectStore(ig,{keyPath:"accession"})});function g6(e){return oi("domain cache read",async()=>{let r=(await A6()).transaction(ig,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n},[])}function h6(e){return oi("domain cache write",async()=>{let r=(await A6()).transaction(ig,"readwrite");for(let n of e)await r.store.put(n);await r.done},void 0)}function ui(e,t){let r=new RegExp(`<${t}>(.*?)</${t}>`,"s").exec(e)?.[1];return r===void 0?void 0:Zu(r)}function nne(e){let t={},r=/<GBQualifier>([\s\S]*?)<\/GBQualifier>/g,n;for(;(n=r.exec(e))!==null;){let o=ui(n[1],"GBQualifier_name"),i=ui(n[1],"GBQualifier_value");o&&i!==void 0&&t[o]===void 0&&(t[o]=i)}return t}function one(e){let t=[],r=[],n=/<GBInterval>([\s\S]*?)<\/GBInterval>/g,o;for(;(o=n.exec(e))!==null;){let i=o[1],s=ui(i,"GBInterval_from"),a=ui(i,"GBInterval_to"),l=ui(i,"GBInterval_point");s&&a?(t.push(Number(s)),r.push(Number(a))):l&&(t.push(Number(l)),r.push(Number(l)))}return t.length>0?{start:Math.min(...t),end:Math.max(...r)}:void 0}var ine=2;function sne(e){let t=ui(e,"GBFeature_key"),r=nne(e),n=r.db_xref,o=one(e);if((t==="Region"||t==="Site")&&n?.startsWith("CDD:")&&o&&o.end-o.start+1>=ine){let i=n.replace("CDD:",""),s=t==="Region",a=r.note?.split(/[[(]/)[0]?.trim(),l=s?r.region_name??i:a||r.site_type||"site",c=s?i:`${i}:${l}`;return{signature:{entry:{name:l,description:r.note??l,accession:c}},locations:[o]}}}function ane(e){let t=new Map,r=/<GBSeq>([\s\S]*?)<\/GBSeq>/g,n;for(;(n=r.exec(e))!==null;){let o=n[1],i=[],s=/<GBFeature>([\s\S]*?)<\/GBFeature>/g,a;for(;(a=s.exec(o))!==null;){let l=sne(a[1]);l&&i.push(l)}for(let l of[ui(o,"GBSeq_accession-version"),ui(o,"GBSeq_primary-accession")])l&&t.set(l,i)}return t}async function y6(e){let t=[...new Set(e)].filter(Boolean),r=new Map,n=await g6(t),o=[];t.forEach((a,l)=>{let c=n[l];c?r.set(a,c.matches):o.push(a)});let i=[],s=100;for(let a=0;a<o.length;a+=s){let l=o.slice(a,a+s),c=await Cs(vc({db:"protein",id:l.join(","),rettype:"gp",retmode:"xml"})),u=ane(c);for(let f of l){let m=u.get(f);m!==void 0&&(r.set(f,m),i.push({accession:f,matches:m}))}}return i.length>0&&await h6(i),r}async function b6(e){let t=e.data.treeMetadata;if(!t)throw new Error("No sequence metadata available to look up domains");let r=JSON.parse(t),n=Object.entries(r).map(([s,a])=>({rowName:s,accession:a.Accession})).filter(s=>!!s.accession);if(n.length===0)throw new Error("No NCBI accessions found in alignment rows");e.setProgress(`Fetching protein domains from NCBI for ${n.length} sequences...`);let o=await y6(n.map(s=>s.accession)),i=n.flatMap(({rowName:s,accession:a})=>(o.get(a)??[]).flatMap(({signature:l,locations:c})=>l.entry?c.map(({start:u,end:f})=>({id:s,accession:l.entry.accession,name:l.entry.name,description:l.entry.description,start:u,end:f})):[]));if(i.length===0)throw new Error("No CDD domain annotations found for these proteins");e.setAnnotations(i)}var cne="jbrowse-msaview-data",lne=1,vs="msa-data",sg=ni(cne,lne,e=>{e.objectStoreNames.contains(vs)||e.createObjectStore(vs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})});function C6(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function x6(e,t){try{let r=await sg(),n={...t,id:e,timestamp:Date.now()};return await r.put(vs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function E6(e){try{let t=await sg(),r=await t.get(vs,e);if(!r)return;try{await t.put(vs,{...r,timestamp:Date.now()})}catch(s){console.warn("Failed to refresh MSA data timestamp:",s)}let{id:n,timestamp:o,...i}=r;return i}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function w6(e){try{await(await sg()).delete(vs,e)}catch(t){console.warn("Failed to delete MSA data:",t)}}async function S6(e=10080*60*1e3){try{let t=await sg(),r=Date.now()-e,i=await t.transaction(vs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}var I6=g(Ve()),v6=g(Hr());mo();function une(e){if(!(e.rows.length<2))try{e.calculateNeighborJoiningTreeFromMSA()}catch(t){console.error(t);try{(0,I6.getSession)(e).notify(`The alignment loaded, but no tree was built. ${t instanceof Error?t.message:String(t)}`,"warning")}catch(r){console.error(r)}}}function sw(e){(0,v6.untracked)(()=>{fne(e)})}function fne({self:e,message:t,launch:r,onLaunched:n}){e.launchController?.abort();let o=new AbortController,{signal:i}=o;e.setLaunchController(o);let s=l=>{i.aborted||l()},a={signal:i,act:s,onProgress:l=>{s(()=>{e.setProgress(l)})},onRid:l=>{s(()=>{e.setRid(l)})}};(async()=>{try{s(()=>{e.setProgress(t),e.setError(void 0)});let l=await r(a);s(()=>{e.setData(l),n()}),l.tree||s(()=>{une(e)})}catch(l){PA(l)||(s(()=>{e.setError(l)}),console.error(l))}finally{s(()=>{e.setProgress(""),e.launchController===o&&e.setLaunchController(void 0)})}})()}function dne(e){let t=e;return t.type==="ProteinView"&&Array.isArray(t.structures)}function B6(e){return e.filter(dne)}var mne="This view's alignment is no longer in browser storage. Stored alignments are kept for 7 days after they were last used, and are lost when site data is cleared.",pne=" Retry runs the original search again and rebuilds it.",Ane=" Relaunch it from the gene to rebuild it.";function R6(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await E6(t);n?(0,ag.transaction)(()=>{n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree),n.treeMetadata&&e.setTreeMetadata(n.treeMetadata),n.gff&&e.setGFF(n.gff),e.setLastStoredData(k6(e))}):(0,ag.transaction)(()=>{e.setDataStoreId(void 0),e.setError(new Error(mne+(e.blastParams??e.orthologParams?pne:Ane)))})}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function k6(e){let{msa:t,tree:r,treeMetadata:n,gff:o}=e.data;return{msa:t,tree:r,treeMetadata:n,gff:o}}function gne(e,t){return!!e&&e.msa===t.msa&&e.tree===t.tree&&e.treeMetadata===t.treeMetadata&&e.gff===t.gff}function Q6(e){let{rows:t,dataStoreId:r,isStoringData:n,lastStoredData:o,init:i}=e,s=k6(e);t.length===0||n||e.msaFilehandle||e.treeFilehandle||i?.msaIndexedLocation||!(s.msa||s.tree)||gne(o,s)||(e.setIsStoringData(!0),(async()=>{try{let a=r??C6();await x6(a,s)&&e.setDataStoreId(a)}catch(a){console.error("Failed to store MSA data to IndexedDB:",a)}finally{(0,ag.transaction)(()=>{e.setLastStoredData(s),e.setIsStoringData(!1)})}})())}function _6(e){e.orthologParams&&!e.launchCompleted&&!D6(e)&&sw({self:e,message:"Resolving orthologs",launch:t=>D4({self:e,scope:t}),onLaunched:()=>{e.setLaunchCompleted(!0)}})}function D6(e){return!!e.connectedTranscript&&!e.connectedFeature}function N6(e){e.blastParams&&!e.launchCompleted&&!D6(e)&&sw({self:e,message:"Submitting query",launch:t=>M4({self:e,scope:t}),onLaunched:()=>{e.setLaunchCompleted(!0)}})}function L6(e){let{rows:t,domainsRequested:r,annotations:n}=e,o=e.data.treeMetadata?.includes('"Accession"')??!1;t.length>0&&o&&n.length===0&&!r&&(e.setDomainsRequested(!0),(async()=>{try{await b6(e)}catch(i){console.error("[msaview-domains] auto-load failed:",i)}finally{e.setProgress("")}})())}function F6(e){let{init:t}=e;if(t){let{msaUrl:r,msaIndexedLocation:n,msaName:o,querySeqName:i}=t,s=!!(n&&o);if(s&&e.data.msa)return;(async()=>{try{if(e.setError(void 0),r){let a=T4(r);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(i&&e.setQuerySeqName(i),r)e.setMSAFilehandle({uri:r,locationType:"UriLocation"});else if(n&&o){let a=await d6({location:n,name:o});if(a)e.setMSA(a);else throw new Error(`No alignment named ${o} in ${n.uri}`)}s||e.setInit(void 0)}catch(a){e.setError(a),console.error(a)}})()}}function P6(e){let t=!1;return()=>{let r=p6({model:e});r!==void 0?(e.setMousePos(r),t=!0):t&&(e.setMousePos(void 0),t=!1)}}function T6(e,t){let{connectedViewId:r,transcriptToMsaMap:n}=e;if(!n||!$A(e))return[];let{g2p:o}=n,i=new Set;for(let s of B6((0,M6.getSession)(e).views))for(let a of s.structures)if(a.connectedViewId===r)for(let l of a[t]??[])for(let c=l.start;c<l.end;c++){let u=o[c],f=u===void 0?void 0:jA(e,u);f!==void 0&&i.add(f)}return[...i]}function hne(e,t){return!e||!t?e===t:e.length===t.length&&e.every((r,n)=>r===t[n])}function O6(e){let t;return()=>{let{connectedViewId:r,transcriptToMsaMap:n}=e;if(!r||!n)return;let o=T6(e,"hoverGenomeHighlights"),i=o.length?[]:T6(e,"clickGenomeHighlights"),s=e.highlightColumns??[],a=o.length?o:i.length?i:s,l=a.length>0?a:void 0;hne(t,l)||(t=l,e.setHighlightedColumns(l))}}function G6(){S6().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}function cg({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,i=e.visibleColToSeqPos(r,t);if(i===void 0)return[];if(o){let s=o.start+i;return s<o.end?[{refName:o.refName,start:s,end:s+1}]:[]}if(n){let{refName:s,p2gCodon:a}=n,l=i+(e.querySeqOffset??0);return lB(a,l)?.map(([c,u])=>({refName:s,start:c,end:u}))??[]}return[]}function H6(e){let t=cg(e),r=t[0],n=t.at(-1);return r&&n?{refName:r.refName,start:r.start,end:n.end}:void 0}var Y6=g(Ai()),cw=g(Ve()),J6=g(Rt()),fg=g(Hr());var j6=g(Ve());$6();f_();function Cne({cds:e,sequence:t,geneticCodeId:r,translExcept:n}){let{codonTable:o,starts:i}=bC(r);return U6({cds:e,sequence:t,codonTable:o,starts:i,translExcept:n})}function V6(e){return`${e.start}-${e.end}`}function xne(e){return e.filter((t,r,n)=>!r||V6(t)!==V6(n[r-1]))}function Ene(e,t){return e.map(r=>({...r,start:t-r.end,end:t-r.start})).toSorted((r,n)=>r.start-n.start)}function lg({feature:e,seq:t,assemblyGeneticCodeId:r}){let{subfeatures:n,start:o,end:i,strand:s}=e.toJSON(),a=xne(n?.toSorted((f,m)=>f.start-m.start).map(f=>({...f,start:f.start-o,end:f.end-o})).filter(f=>f.type==="CDS")??[]),l=e.get("subfeatures")?.find(f=>f.get("type")?.toLowerCase()==="cds"),c=yC(e.get("transl_table"))??yC(l?.get("transl_table"))??r,u=e.get("transl_except")??l?.get("transl_except");return Cne({cds:s===-1?Ene(a,t.length):a,sequence:s===-1?(0,j6.revcom)(t):t,geneticCodeId:c,translExcept:u?l_({raw:u,featureStart:o,featureLength:i-o,strand:s}):void 0})}var W6=g(Ai());async function ug({start:e,end:t,refName:r,session:n,assemblyName:o}){let{assemblyManager:i,rpcManager:s}=n,a=await i.waitForAssembly(o);if(!a)throw new Error("assembly not found");let l="getSequence",c={adapterConfig:(0,W6.getConf)(a,["sequence","adapter"]),sessionId:l,regions:[{start:e,end:t,refName:a.getCanonicalRefName(r)??r,assemblyName:o}]};return{seq:(await s.call(l,"CoreGetFeatures",c))[0]?.get("seq")??"",assemblyGeneticCodeId:wne(a,r)}}function wne(e,t){return e.getGeneticCodeId?.(t)}function q6(e){return e.replace(/\.\d+$/,"")}function Sne(e,t){let r=q6(t);return[e.get("name"),e.get("id"),e.get("transcript_id"),e.id()].some(n=>typeof n=="string"&&(n===t||q6(n)===r))}function z6(e){return e.map(t=>({assemblyName:t.assemblyName,refName:t.refName,start:Math.floor(t.start),end:Math.ceil(t.end)}))}function Ine(e){let t=z6(e.dynamicBlocks?.contentBlocks??[]),r=z6(e.displayedRegions);return t.length>0?[t,r]:[r]}function K6(e){return e.filter(t=>t.type==="FeatureTrack")}async function vne(e,t){let r=e.connectedView,n=(0,cw.getSession)(e),o="msaview-connectedTranscript",i=K6(r.tracks);for(let s of Ine(r))for(let a of i){let l={adapterConfig:(0,Y6.getConf)(a,"adapter"),sessionId:o,regions:s},c=await n.rpcManager.call(o,"CoreGetFeatures",l);for(let u of c){let f=gE(u).find(m=>Sne(m,t));if(f)return f}}}async function Bne(e,t){let{start:r,end:n,refName:o}=t.toJSON(),i=e.connectedView.assemblyNames[0],{seq:s,assemblyGeneticCodeId:a}=await ug({start:r,end:n,refName:o,assemblyName:i,session:(0,cw.getSession)(e)});return lg({seq:s,feature:t,assemblyGeneticCodeId:a})}var aw=new WeakMap;async function Tne({self:e,transcriptId:t,blastParams:r,orthologParams:n,isCurrent:o}){let i=K6(e.connectedView.tracks).length;try{e.setProgress(`Looking up ${t} in the genome view...`);let s=await vne(e,t);if(!s)throw new Error(`Transcript "${t}" was not found in the ${i} feature track(s) open in the connected genome view. Open the gene track that carries it, and make sure the view is on its locus.`);let a=await Bne(e,s);if(!a)throw new Error(`Transcript "${t}" has no CDS to translate`);if(!o())return;let l=s.toJSON();(0,fg.transaction)(()=>{e.setProgress(""),r&&!r.proteinSequence&&e.setBlastParams({...r,selectedTranscript:l,proteinSequence:a}),n&&!n.proteinSequence&&e.setOrthologParams({...n,selectedTranscript:l,proteinSequence:a}),e.setConnectedFeature(l)})}catch(s){console.error(s),o()&&(e.setProgress(""),e.setError(s))}}function X6(e){let{connectedTranscript:t,connectedFeature:r,connectedView:n,blastParams:o,orthologParams:i}=e;if(!t||r||!n?.initialized||n.tracks.length===0)return;let s=(aw.get(e)??0)+1;aw.set(e,s),(0,fg.untracked)(()=>{Tne({self:e,transcriptId:t,blastParams:o,orthologParams:i,isCurrent:()=>(0,J6.isAlive)(e)&&aw.get(e)===s})})}function lw(){return Ke.types.compose(Z6.BaseViewModel,vA(),Ke.types.model("MsaView",{connectedViewId:Ke.types.maybe(Ke.types.string),connectedFeature:Ke.types.frozen(),connectedTranscript:Ke.types.maybe(Ke.types.string),blastParams:Ke.types.frozen(),orthologParams:Ke.types.frozen(),querySeqName:"QUERY",querySeqOffset:0,uniprotId:Ke.types.maybe(Ke.types.string),zoomToBaseLevel:!1,init:Ke.types.frozen(),dataStoreId:Ke.types.maybe(Ke.types.string),launchCompleted:!1,mafRegion:Ke.types.frozen()})).volatile(()=>({rid:void 0,progress:"",loadingStoredData:!1,isStoringData:!1,lastStoredData:void 0,launchController:void 0,domainsRequested:!1})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?cB(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,e8.getSession)(e);return t.find(r=>r.id===e.connectedViewId)}})).views(e=>({get connectedHoverHighlights(){let{mouseCol:t}=e;return t===void 0?[]:cg({model:e,coord:t})},get connectedClickHighlights(){let{mouseClickCol:t}=e;return t===void 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t=e.data.treeMetadata;if(!t)throw new Error("No sequence metadata available to look up domains");let r=JSON.parse(t),n=Object.entries(r).map(([s,a])=>({rowName:s,accession:a.Accession})).filter(s=>!!s.accession);if(n.length===0)throw new Error("No NCBI accessions found in alignment rows");e.setProgress(`Fetching protein domains from NCBI for ${n.length} sequences...`);let o=await y6(n.map(s=>s.accession)),i=n.flatMap(({rowName:s,accession:a})=>(o.get(a)??[]).flatMap(({signature:l,locations:c})=>l.entry?c.map(({start:u,end:f})=>({id:s,accession:l.entry.accession,name:l.entry.name,description:l.entry.description,start:u,end:f})):[]));if(i.length===0)throw new Error("No CDD domain annotations found for these proteins");e.setAnnotations(i)}var cne="jbrowse-msaview-data",lne=1,vs="msa-data",sg=ni(cne,lne,e=>{e.objectStoreNames.contains(vs)||e.createObjectStore(vs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})});function 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Stored alignments are kept for 7 days after they were last used, and are lost when site data is cleared.",pne=" Retry runs the original search again and rebuilds it.",Ane=" Relaunch it from the gene to rebuild it.";function R6(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await E6(t);n?(0,ag.transaction)(()=>{n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree),n.treeMetadata&&e.setTreeMetadata(n.treeMetadata),n.gff&&e.setGFF(n.gff),e.setLastStoredData(k6(e))}):(0,ag.transaction)(()=>{e.setDataStoreId(void 0),e.setError(new Error(mne+(e.blastParams??e.orthologParams?pne:Ane)))})}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function k6(e){let{msa:t,tree:r,treeMetadata:n,gff:o}=e.data;return{msa:t,tree:r,treeMetadata:n,gff:o}}function gne(e,t){return!!e&&e.msa===t.msa&&e.tree===t.tree&&e.treeMetadata===t.treeMetadata&&e.gff===t.gff}function 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L6(e){let{rows:t,domainsRequested:r,annotations:n}=e,o=e.data.treeMetadata?.includes('"Accession"')??!1;t.length>0&&o&&n.length===0&&!r&&(e.setDomainsRequested(!0),(async()=>{try{await b6(e)}catch(i){console.error("[msaview-domains] auto-load failed:",i)}finally{e.setProgress("")}})())}function F6(e){let{init:t}=e;if(t){let{msaUrl:r,msaIndexedLocation:n,msaName:o,querySeqName:i}=t,s=!!(n&&o);if(s&&e.data.msa)return;(async()=>{try{if(e.setError(void 0),r){let a=T4(r);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(i&&e.setQuerySeqName(i),r)e.setMSAFilehandle({uri:r,locationType:"UriLocation"});else if(n&&o){let a=await d6({location:n,name:o});if(a)e.setMSA(a);else throw new Error(`No alignment named ${o} in ${n.uri}`)}s||e.setInit(void 0)}catch(a){e.setError(a),console.error(a)}})()}}function P6(e){let t=!1;return()=>{let r=p6({model:e});r!==void 0?(e.setMousePos(r),t=!0):t&&(e.setMousePos(void 0),t=!1)}}function T6(e,t){let{connectedViewId:r,transcriptToMsaMap:n}=e;if(!n||!$A(e))return[];let{g2p:o}=n,i=new Set;for(let s of B6((0,M6.getSession)(e).views))for(let a of s.structures)if(a.connectedViewId===r)for(let l of a[t]??[])for(let c=l.start;c<l.end;c++){let u=o[c],f=u===void 0?void 0:jA(e,u);f!==void 0&&i.add(f)}return[...i]}function hne(e,t){return!e||!t?e===t:e.length===t.length&&e.every((r,n)=>r===t[n])}function O6(e){let t;return()=>{let{connectedViewId:r,transcriptToMsaMap:n}=e;if(!r||!n)return;let o=T6(e,"hoverGenomeHighlights"),i=o.length?[]:T6(e,"clickGenomeHighlights"),s=e.highlightColumns??[],a=o.length?o:i.length?i:s,l=a.length>0?a:void 0;hne(t,l)||(t=l,e.setHighlightedColumns(l))}}function G6(){S6().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}function cg({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,i=e.visibleColToSeqPos(r,t);if(i===void 0)return[];if(o){let s=o.start+i;return s<o.end?[{refName:o.refName,start:s,end:s+1}]:[]}if(n){let{refName:s,p2gCodon:a}=n,l=i+(e.querySeqOffset??0);return lB(a,l)?.map(([c,u])=>({refName:s,start:c,end:u}))??[]}return[]}function H6(e){let t=cg(e),r=t[0],n=t.at(-1);return r&&n?{refName:r.refName,start:r.start,end:n.end}:void 0}var Y6=g(Ai()),cw=g(Ve()),J6=g(Rt()),fg=g(Hr());var j6=g(Ve());$6();f_();function Cne({cds:e,sequence:t,geneticCodeId:r,translExcept:n}){let{codonTable:o,starts:i}=bC(r);return U6({cds:e,sequence:t,codonTable:o,starts:i,translExcept:n})}function V6(e){return`${e.start}-${e.end}`}function xne(e){return e.filter((t,r,n)=>!r||V6(t)!==V6(n[r-1]))}function Ene(e,t){return e.map(r=>({...r,start:t-r.end,end:t-r.start})).toSorted((r,n)=>r.start-n.start)}function lg({feature:e,seq:t,assemblyGeneticCodeId:r}){let{subfeatures:n,start:o,end:i,strand:s}=e.toJSON(),a=xne(n?.toSorted((f,m)=>f.start-m.start).map(f=>({...f,start:f.start-o,end:f.end-o})).filter(f=>f.type==="CDS")??[]),l=e.get("subfeatures")?.find(f=>f.get("type")?.toLowerCase()==="cds"),c=yC(e.get("transl_table"))??yC(l?.get("transl_table"))??r,u=e.get("transl_except")??l?.get("transl_except");return Cne({cds:s===-1?Ene(a,t.length):a,sequence:s===-1?(0,j6.revcom)(t):t,geneticCodeId:c,translExcept:u?l_({raw:u,featureStart:o,featureLength:i-o,strand:s}):void 0})}var W6=g(Ai());async function ug({start:e,end:t,refName:r,session:n,assemblyName:o}){let{assemblyManager:i,rpcManager:s}=n,a=await i.waitForAssembly(o);if(!a)throw new Error("assembly not found");let l="getSequence",c={adapterConfig:(0,W6.getConf)(a,["sequence","adapter"]),sessionId:l,regions:[{start:e,end:t,refName:a.getCanonicalRefName(r)??r,assemblyName:o}]};return{seq:(await s.call(l,"CoreGetFeatures",c))[0]?.get("seq")??"",assemblyGeneticCodeId:wne(a,r)}}function wne(e,t){return e.getGeneticCodeId?.(t)}function q6(e){return e.replace(/\.\d+$/,"")}function Sne(e,t){let r=q6(t);return[e.get("name"),e.get("id"),e.get("transcript_id"),e.id()].some(n=>typeof n=="string"&&(n===t||q6(n)===r))}function z6(e){return e.map(t=>({assemblyName:t.assemblyName,refName:t.refName,start:Math.floor(t.start),end:Math.ceil(t.end)}))}function Ine(e){let t=z6(e.dynamicBlocks?.contentBlocks??[]),r=z6(e.displayedRegions);return t.length>0?[t,r]:[r]}function K6(e){return e.filter(t=>t.type==="FeatureTrack")}async function vne(e,t){let r=e.connectedView,n=(0,cw.getSession)(e),o="msaview-connectedTranscript",i=K6(r.tracks);for(let s of Ine(r))for(let a of i){let l={adapterConfig:(0,Y6.getConf)(a,"adapter"),sessionId:o,regions:s},c=await n.rpcManager.call(o,"CoreGetFeatures",l);for(let u of c){let f=gE(u).find(m=>Sne(m,t));if(f)return f}}}async function Bne(e,t){let{start:r,end:n,refName:o}=t.toJSON(),i=e.connectedView.assemblyNames[0],{seq:s,assemblyGeneticCodeId:a}=await ug({start:r,end:n,refName:o,assemblyName:i,session:(0,cw.getSession)(e)});return lg({seq:s,feature:t,assemblyGeneticCodeId:a})}var aw=new WeakMap;async function Tne({self:e,transcriptId:t,blastParams:r,orthologParams:n,isCurrent:o}){let i=K6(e.connectedView.tracks).length;try{e.setProgress(`Looking up ${t} in the genome view...`);let s=await vne(e,t);if(!s)throw new Error(`Transcript "${t}" was not found in the ${i} feature track(s) open in the connected genome view. Open the gene track that carries it, and make sure the view is on its locus.`);let a=await Bne(e,s);if(!a)throw new Error(`Transcript "${t}" has no CDS to translate`);if(!o())return;let l=s.toJSON();(0,fg.transaction)(()=>{e.setProgress(""),r&&!r.proteinSequence&&e.setBlastParams({...r,selectedTranscript:l,proteinSequence:a}),n&&!n.proteinSequence&&e.setOrthologParams({...n,selectedTranscript:l,proteinSequence:a}),e.setConnectedFeature(l)})}catch(s){console.error(s),o()&&(e.setProgress(""),e.setError(s))}}function X6(e){let{connectedTranscript:t,connectedFeature:r,connectedView:n,blastParams:o,orthologParams:i}=e;if(!t||r||!n?.initialized||n.tracks.length===0)return;let s=(aw.get(e)??0)+1;aw.set(e,s),(0,fg.untracked)(()=>{Tne({self:e,transcriptId:t,blastParams:o,orthologParams:i,isCurrent:()=>(0,J6.isAlive)(e)&&aw.get(e)===s})})}function lw(){return Ke.types.compose(Z6.BaseViewModel,vA(),Ke.types.model("MsaView",{connectedViewId:Ke.types.maybe(Ke.types.string),connectedFeature:Ke.types.frozen(),connectedTranscript:Ke.types.maybe(Ke.types.string),blastParams:Ke.types.frozen(),orthologParams:Ke.types.frozen(),querySeqName:"QUERY",querySeqOffset:0,uniprotId:Ke.types.maybe(Ke.types.string),zoomToBaseLevel:!1,init:Ke.types.frozen(),dataStoreId:Ke.types.maybe(Ke.types.string),launchCompleted:!1,mafRegion:Ke.types.frozen()})).volatile(()=>({rid:void 0,progress:"",loadingStoredData:!1,isStoringData:!1,lastStoredData:void 0,launchController:void 0,domainsRequested:!1})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?cB(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,e8.getSession)(e);return t.find(r=>r.id===e.connectedViewId)}})).views(e=>({get connectedHoverHighlights(){let{mouseCol:t}=e;return t===void 0?[]:cg({model:e,coord:t})},get connectedClickHighlights(){let{mouseClickCol:t}=e;return t===void 0?[]:cg({model:e,coord:t})},get connectedHighlights(){return[...this.connectedHoverHighlights,...this.connectedClickHighlights]}})).views(e=>({get hostRestoresData(){let{msaIndexedLocation:t,msaName:r}=e.init??{};return e.hostCarriesData||!!(t&&r)}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setBlastParams(t){e.blastParams=t},setConnectedFeature(t){e.connectedFeature=t},setOrthologParams(t){e.orthologParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setLaunchCompleted(t){e.launchCompleted=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},setLastStoredData(t){e.lastStoredData=t},setLaunchController(t){e.launchController=t},cancelLaunch(){e.launchController?.abort(),e.launchController=void 0,e.blastParams=void 0,e.orthologParams=void 0,e.init=void 0,e.launchCompleted=!1,e.progress="",e.rid=void 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click?",type:"checkbox",checked:e.zoomToBaseLevel,onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}}]}}}).actions(e=>({afterCreate(){G6(),(0,Ke.addDisposer)(e,()=>{e.launchController?.abort()});for(let t of[R6,Q6,X6,N6,_6,F6,L6])(0,Ke.addDisposer)(e,(0,dg.autorun)(()=>{t(e)}));(0,Ke.addDisposer)(e,(0,dg.autorun)(P6(e))),(0,Ke.addDisposer)(e,(0,dg.autorun)(O6(e)))}}))}function Dc(e){return e.type==="MsaView"}var df=g(k()),a8=g(Y());var uw=g(k()),n8=g(Ve()),fw=g(Y());var r8=g(Bt()),mg=(0,r8.makeStyles)()({highlight:{height:"100%",background:"rgba(255,255,0,0.2)",border:"1px solid rgba(50,50,0,0.2)",position:"absolute",zIndex:99,textAlign:"center",pointerEvents:"none",overflow:"hidden"}});var Mne=(0,fw.observer)(function({model:e}){let{hovered:t,views:r}=(0,n8.getSession)(e);return r.some(o=>Dc(o)&&o.connectedViewId===e.id)&&Es(t)?uw.default.createElement(Rne,{model:e,hovered:t}):null}),Rne=(0,fw.observer)(function({model:e,hovered:t}){let{classes:r}=mg(),{offsetPx:n}=e,{coord:o,refName:i}=t.hoverPosition,s=e.bpToPx({refName:i,coord:o-1}),a=e.bpToPx({refName:i,coord:o});if(s&&a){let l=Math.max(Math.abs(a.offsetPx-s.offsetPx),4),c=Math.min(s.offsetPx,a.offsetPx)-n;return uw.default.createElement("div",{className:r.highlight,style:{left:c,width:l}})}return null}),o8=Mne;var ff=g(k()),i8=g(Ve()),dw=g(Y());var kne=(0,dw.observer)(function({model:t}){let{views:r,hovered:n}=(0,i8.getSession)(t),o=r.filter(Dc).find(s=>s.connectedViewId===t.id),i=[...o?.connectedClickHighlights??[],...Es(n)?[]:o?.connectedHoverHighlights??[]];return i.length?ff.default.createElement(Qne,{model:t,highlights:i}):null}),Qne=(0,dw.observer)(function({model:e,highlights:t}){let{classes:r}=mg(),{offsetPx:n}=e;return ff.default.createElement(ff.default.Fragment,null,t.map((o,i)=>{let s=e.bpToPx({refName:o.refName,coord:o.start}),a=e.bpToPx({refName:o.refName,coord:o.end});if(s&&a){let l=Math.max(Math.abs(a.offsetPx-s.offsetPx),4),c=Math.min(s.offsetPx,a.offsetPx)-n;return ff.default.createElement("div",{key:`${o.refName}-${o.start}-${o.end}-${i}`,className:r.highlight,style:{left:c,width:l}})}return null}))}),s8=kne;var _ne=(0,a8.observer)(function({model:t}){return df.default.createElement(df.default.Fragment,null,df.default.createElement(s8,{model:t}),df.default.createElement(o8,{model:t}))}),c8=_ne;function mw(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t,{model:r})=>{let{views:n}=(0,u8.getSession)(r);return n.some(i=>Dc(i)&&i.connectedViewId===r.id)?[...t,l8.default.createElement(c8,{key:"highlight_protein_viewer_msaview",model:r})]:t})}var y8=g(R0());var f8=g(Ai());function pw(e){let t=e.getAdapterType("BgzipFastaAdapter");return(0,f8.ConfigurationSchema)("BgzipFastaMsaAdapter",{msaRegex:{type:"string",defaultValue:"_"}},{baseConfiguration:t.configSchema})}function Aw(e){return e.addAdapterType(()=>new y8.AdapterType({name:"BgzipFastaMsaAdapter",configSchema:pw(e),adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>Promise.resolve().then(()=>(h8(),g8)).then(t=>t.default)}))}var kg=g(Ve());oe();var b8=g(O(),1),C8=$((0,b8.jsx)("path",{d:"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z"}),"Add");var Dne=/gene(_segment)?$|rna$|transcript/;function Ag(e){return typeof e=="string"&&Dne.test(e.toLowerCase())}function Nne(e){return e.get("type")?.toLowerCase()==="cds"}function gg(e){return Nne(e)||!!e.get("subfeatures")?.some(gg)}function x8(e){return!!e.get("subfeatures")?.length&&!gg(e)}function E8(e){let t=e;for(let r=t.parent?.();r&&Ag(r.get("type"));r=r.parent?.())t=r;return t}var nt=g(k()),jH=g(Ye()),WH=g(Ve()),Rs=g(H());var Fr=g(k());I8();var Sg=g(H()),bH=g(Bt());wc();Ju();var Pe=g(k());qp();var Nr=g(H()),sH=g(Y()),aH=g(Bt());var gw=g(k()),v8=g(H());function Lne({children:e,...t}){return gw.default.createElement("div",null,gw.default.createElement(v8.TextField,{...t},e))}var Se=Lne;var hw=g(k()),B8=g(Ye()),T8=g(H()),M8=g(Bt()),Fne=(0,M8.makeStyles)()({dialogContent:{width:"80em"}});function Kr({error:e,children:t}){let{classes:r}=Fne();return hw.default.createElement(T8.DialogContent,{className:r.dialogContent},e?hw.default.createElement(B8.ErrorMessage,{error:e}):null,t)}var yw=g(k()),R8=g(Ye()),k8=g(H());function ho({status:e}){return e==="loading"?yw.default.createElement(R8.LoadingEllipses,{message:"Translating transcript"}):e==="missing"?yw.default.createElement(k8.Typography,{color:"textSecondary",variant:"body2"},"no coding sequence to align"):null}var fi=g(k()),G8=g(Ve()),bo=g(H());var Pne=["stack","splitRight","newTab"],Q8="splitRight",D8="msaView-launchPlacement";function hg(e,t){return t in e&&typeof e[t]=="function"}var _8=!1;function N8(e){return hg(e,"setUseWorkspaces")&&hg(e,"setPendingMove")}function One(e){let t=hg(e,"setUseWorkspaces"),r=hg(e,"setPendingMove");return t!==r&&!_8&&(_8=!0,console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ${r?"setUseWorkspaces":"setPendingMove"}, so the MSA view was stacked instead of tiled. 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+`)?e:void 0,o=t?.trimStart().startsWith("(")?t:void 0,i=n||o?{...r.data,...n?{msa:n}:{},...o?{tree:o}:{}}:r.data;return{...r,data:i,...e&&!n?{msaFileLocation:{uri:e}}:{},...t&&!o?{treeFileLocation:{uri:t}}:{},querySeqName:r.querySeqName??r.query}}function _w(e){e.addToExtensionPoint("LaunchView-MsaView",t=>{let{session:r,query:n,data:o,msaFileLocation:i,msaIndexedLocation:s,msaName:a,treeFileLocation:l,querySeqName:c,searchParams:u,...f}=Roe(t);if(!o&&!i&&!s&&!f.orthologParams&&!u)throw new Error("No MSA data, file location, orthologParams or searchParams provided when launching MSA view");let m={msaUrl:i?.uri,msaIndexedLocation:s,msaName:a,querySeqName:c};return Lc(r,{...Ny({...f,query:n}),...u?{blastParams:u}:{},data:o,...l?{treeFilehandle:{...l,locationType:"UriLocation"}}:{},...Object.values(m).some(d=>d!==void 0)?{init:m}:{}}),t})}var l9=g(k()),u9=g(YH());var Foe=(0,l9.lazy)(()=>Promise.resolve().then(()=>(c9(),a9)));function Lw(e){e.addViewType(()=>new u9.default({name:"MsaView",stateModel:lw(),ReactComponent:Foe}))}var f9="3.8.0";var Dg=class extends d9.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=f9;this.rootConfigurationSchema=r=>({msa:(0,Fw.ConfigurationSchema)("MSA",{datasets:Pw.types.maybe(Pw.types.array((0,Fw.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Lw(r),Qw(r),_w(r),mw(r),Aw(r)}configure(r){try{(0,m9.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:sB,onClick:n=>{Lc(n,{})}})}catch(n){console.error("jbrowse-plugin-msaview: could not add the Add menu item",n)}}};return O9(Poe);})();
 /*! Bundled license information:
 
 react-is/cjs/react-is.production.js: