@apollo-annotation/jbrowse-plugin-apollo 0.2.1 → 0.2.2

package/dist/jbrowse-plugin-apollo.cjs.production.min.js

@@ -1,2 +1,2 @@
-"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@apollo-annotation/common"),t=require("@apollo-annotation/shared"),n=require("@jbrowse/core/configuration"),a=require("@jbrowse/core/pluggableElementTypes"),o=require("@jbrowse/core/Plugin"),r=require("@jbrowse/core/util"),s=require("@mui/icons-material/Add"),l=require("mobx"),i=require("mobx-state-tree"),c=require("socket.io-client"),u=require("@gmod/gff"),d=require("@mui/icons-material/Link"),f=require("@mui/material"),m=require("@mui/material/InputAdornment"),g=require("@mui/material/LinearProgress"),p=require("bson-objectid"),h=require("react"),y=require("@jbrowse/core/ui"),b=require("@mui/icons-material/Close"),S=require("mobx-react"),w=require("tss-react/mui"),v=require("@jbrowse/core/util/types/mst"),C=require("idb/with-async-ittr"),E=require("@jbrowse/core/util/aborting"),x=require("jsonpath"),A=require("@jbrowse/core/util/io"),T=require("fast-deep-equal/es6"),k=require("file-saver"),N=require("@mui/material/Checkbox"),R=require("@mui/material/FormControlLabel"),D=require("@mui/icons-material/Delete"),F=require("@mui/x-data-grid"),M=require("@mui/material/utils"),I=require("autosuggest-highlight/match"),L=require("autosuggest-highlight/parse"),q=require("nanoid"),P=require("@mui/icons-material/AccountCircle"),U=require("@jbrowse/core/pluggableElementTypes/AdapterType"),B=require("@jbrowse/core/data_adapters/BaseAdapter"),_=require("@jbrowse/core/util/rxjs"),j=require("@jbrowse/core/util/simpleFeature"),O=require("@jbrowse/core/TextSearch/BaseResults"),$=require("@apollo-annotation/mst"),G=require("@jbrowse/core/util/tracks"),W=require("@mui/icons-material/Clear"),H=require("@mui/icons-material/UnfoldLess"),z=require("@mui/icons-material/ExpandLess"),V=require("@mui/icons-material/ExpandMore"),J=require("@mui/icons-material/Error"),X=require("@mui/icons-material/Save");function Y(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}function K(e){if(e&&e.__esModule)return e;var t=Object.create(null);return e&&Object.keys(e).forEach((function(n){if("default"!==n){var a=Object.getOwnPropertyDescriptor(e,n);Object.defineProperty(t,n,a.get?a:{enumerable:!0,get:function(){return e[n]}})}})),t.default=e,t}var Z=Y(o),Q=Y(s),ee=Y(u),te=Y(d),ne=Y(m),ae=Y(g),oe=Y(p),re=Y(h),se=K(h),le=Y(b),ie=Y(x),ce=Y(T),ue=Y(N),de=Y(R),fe=Y(D),me=Y(I),ge=Y(L),pe=Y(P),he=Y(U),ye=Y(j),be=Y(O),Se=Y(W),we=Y(H),ve=Y(z),Ce=Y(V),Ee=Y(J),xe=Y(X);const Ae=n.ConfigurationSchema("ApolloInternetAccount",{baseURL:{description:"Location of Apollo server",type:"string",defaultValue:""},tokenType:{description:"A custom name for a token to include in the header",type:"string",defaultValue:"Bearer"}},{baseConfiguration:a.BaseInternetAccountConfig,explicitlyTyped:!0});async function Te(e,n,a){const 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oe.default).toHexString(),assemblyName:c,externalLocation:{fa:k,fai:R,...F?{gzi:F}:{}}});else{const e={assembly:(new oe.default).toHexString(),assemblyName:c,fileIds:{fa:u}};p=S===Fe.GFF3&&v?new t.AddAssemblyAndFeaturesFromFileChange({typeName:"AddAssemblyAndFeaturesFromFileChange",...e}):new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",...e})}r.done(i),await e.submit(p,{internetAccountId:g,updateJobsManager:!0}),x(!1),L(!1)}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},l.length>1?re.default.createElement(re.default.Fragment,null,re.default.createElement(f.DialogContentText,null,"Select account"),re.default.createElement(f.Select,{value:A.internetAccountId,onChange:function(e){x(!1);const t=l.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);T(t)},disabled:E&&!d},r.map((e=>re.default.createElement(f.MenuItem,{key:e.id,value:e.internetAccountId},e.name))))):null,re.default.createElement(f.TextField,{margin:"dense",id:"name",label:"Assembly name",type:"TextField",fullWidth:!0,variant:"outlined",onChange:e=>{x(!1),u(e.target.value),function(e){const{assemblies:t}=o;t.find((t=>n.readConfObject(t,"displayName")===e))?(p(!1),m(`Assembly ${e} already exists.`)):(p(!0),m(""))}(e.target.value)},disabled:E&&!d}),re.default.createElement(f.FormControl,{style:{marginTop:20}},re.default.createElement(f.FormLabel,null,"Select GFF3, FASTA or EXTERNAL 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Set(["i","me","my","myself","we","our","ours","ourselves","you","your","yours","yourself","yourselves","he","him","his","himself","she","her","hers","herself","it","its","itself","they","them","their","theirs","themselves","what","which","who","whom","this","that","these","those","am","is","are","was","were","be","been","being","have","has","had","having","do","does","did","doing","a","an","the","and","but","if","or","because","as","until","while","of","at","by","for","with","about","against","between","into","through","during","before","after","above","below","to","from","up","down","in","out","on","off","over","under","again","further","then","once","here","there","when","where","why","how","all","any","both","each","few","more","most","other","some","such","no","nor","not","only","own","same","so","than","too","very","s","t","can","will","just","don","should","now",..."1234567890"]);function Le(e,t){for(const[n,a]of t.entries())if(e.startsWith(a))return e.replace(a,n);return e}const qe="$PREFIXED_ID";function Pe(e,t,n){return t===qe?[Le(e.id,n)]:ie.default.query(e,t)}function Ue(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!Ie.has(e)))}function*Be(e){for(const t of e)yield*Ue(t)}function*_e(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=ie.default.query(t,"$..*");yield*_e(e)}}function*je(e,t,n){for(const a of t){const t=Pe(e,a,n);if(t.length>0)for(const e of Be(_e(t)))yield[a,e]}}async function Oe(e,t,n){const a=await this.db,o=t??a.transaction(["nodes"]);E.checkAbortSignal(n);const r=[...Ue(e)],s=[],l=new Map;s.push(...r.map((async(e,t)=>{E.checkAbortSignal(n);const a=o.objectStore("nodes").index("full-text-words");for await(const o of a.iterate(IDBKeyRange.bound(e,`${e}￿`,!1,!1))){E.checkAbortSignal(n);const e=o.value,a=l.get(e.id)??[e,new Set];a[1].add(t),l.set(e.id,a)}}))),await Promise.all(s),E.checkAbortSignal(n);const i=[];for(const[,[e,t]]of l)E.checkAbortSignal(n),i.push(...$e(this.textIndexFields,e,t,r,this.prefixes));return i.sort(((e,t)=>t.score-e.score)),i.slice(0,this.options.maxSearchResults??this.DEFAULT_MAX_SEARCH_RESULTS)}function $e(e,t,n,a,o){const r=[...n].sort().map((e=>a[e])),s=r.map((e=>{const t=e.replaceAll(/[$()*+./?[\\\]^{|}-]/g,String.raw`\$&`);return new RegExp(`\\b${t}`,"gi")}));let l=[],i=0;for(const[n,r]of e.entries()){const c=new Set,u=e.length-n-1,d=[..._e(Pe(t,r.jsonPath,o))];for(const e of d){let n=0;const o=[];for(const[t,r]of s.entries())for(const s of e.matchAll(r)){n+=1+1*u,c.add(t);const r=s.index,l=a[t];void 0!==r&&(n+=.01*l.length,n+=l.length/e.length*100*.05,o.push({wordIndex:t,position:r}))}n+=100*c.size,i<n&&(i=n),o.sort(((e,t)=>e.position-t.position)),o.length>0&&l.push({term:t,field:r,str:e,score:n,wordMatches:o})}}l=l.filter((e=>e.score===i));for(const e of l){const{wordMatches:t}=e;for(let n=0;n<t.length-1;n++){const a=t[n],o=t[n+1],s=o.wordIndex-a.wordIndex;if(1===s||-1===s){e.score+=1,1===s&&(e.score+=1);const t=Math.abs(o.position-(a.position+r[a.wordIndex].length))-1;e.score-=.05*t}}}return l}function Ge(e){return"string"==typeof e.id}function We(e){return"string"==typeof e.sub&&"string"==typeof e.pred&&"string"==typeof e.obj}function He(e){return Boolean(e.meta?.deprecated)}async function ze(e){return C.openDB(e,2,{upgrade(e,t,n,a,o){if(t<2&&(e.objectStoreNames.contains("meta")&&e.deleteObjectStore("meta"),e.objectStoreNames.contains("nodes")&&e.deleteObjectStore("nodes"),e.objectStoreNames.contains("edges")&&e.deleteObjectStore("edges")),e.objectStoreNames.contains("meta")||e.createObjectStore("meta"),!e.objectStoreNames.contains("nodes")){e.createObjectStore("nodes",{keyPath:"id"});const t=a.objectStore("nodes");t.createIndex("by-label","lbl"),t.createIndex("by-type","type"),t.createIndex("by-synonym",["meta","synonyms","val"]),t.createIndex("full-text-words","fullTextWords",{multiEntry:!0})}if(!e.objectStoreNames.contains("edges")){e.createObjectStore("edges",{autoIncrement:!0});const t=a.objectStore("edges");t.createIndex("by-subject","sub"),t.createIndex("by-object","obj"),t.createIndex("by-predicate","pred")}}})}function Ve(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function Je(e){const t=Date.now();let n;try{n=JSON.parse(await A.openLocation(this.sourceLocation).readFile("utf8"))}catch{throw new Error("Error in loading ontology")}const a=Date.now(),[o,...r]=n.graphs??[];if(o){if(r.length>0)throw new Error("multiple graphs not supported");try{const n=e.transaction(["meta","nodes","edges"],"readwrite");await n.objectStore("meta").clear(),await n.objectStore("nodes").clear(),await n.objectStore("edges").clear();const r=n.objectStore("nodes"),s=Xe.call(this).map((e=>e.jsonPath));for(const e of o.nodes??[])Ge(e)&&await r.add({...e,fullTextWords:Ve(je(e,s,this.prefixes))});const l=n.objectStore("edges");for(const e of o.edges??[])We(e)&&await l.add(e);await n.done;const i=e.transaction("meta","readwrite");await i.objectStore("meta").add({ontologyRecord:{name:this.ontologyName,version:this.ontologyVersion,sourceLocation:this.sourceLocation},storeOptions:this.options,graphMeta:o.meta,timestamp:String(new Date),schemaVersion:2,timings:{overall:Date.now()-t,load:Date.now()-a}},"meta"),await i.done}catch(t){throw await e.transaction("meta","readwrite").objectStore("meta").clear(),t}}}function Xe(){return[{displayName:"ID",jsonPath:qe},...this.options.textIndexing?.indexFields??et]}async function Ye(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&ce.default(this.options.prefixes,t.storeOptions.prefixes)&&ce.default(this.options.textIndexing,t.storeOptions.textIndexing)}class Ke{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=Je;getTermsByFulltext=Oe;openDatabase=ze;isDatabaseCurrent=Ye;get textIndexFields(){return Xe.call(this)}get prefixes(){return this.options.prefixes??new Map}DEFAULT_MAX_SEARCH_RESULTS=100;constructor(e,t,n,a){this.ontologyName=e,this.ontologyVersion=t,this.sourceLocation=n,this.db=this.prepareDatabase(),this.options=a??{}}validate(){const e=[],{sourceLocation:t,sourceType:n}=this;return n?"obo-graph-json"!==n&&e.push(new Error(`ontology source file ${JSON.stringify(t)} has type ${n}, which is not yet supported`)):e.push(new Error(`unable to determine format of ontology source file ${JSON.stringify(t)}, file name must end with ".json", ".obo", or ".owl"`)),e}get sourceType(){if(r.isUriLocation(this.sourceLocation)){if(this.sourceLocation.uri.endsWith(".json"))return"obo-graph-json"}else if(r.isLocalPathLocation(this.sourceLocation)&&this.sourceLocation.localPath.endsWith(".json"))return"obo-graph-json"}get dbName(){return`Apollo Ontology "${this.ontologyName}" "${this.ontologyVersion}"`}async prepareDatabase(){const e=this.validate();if(e.length>0)throw e;const t=await this.openDatabase(this.dbName);if(await this.isDatabaseCurrent(t))return t;try{const{sourceLocation:e,sourceType:n}=this;if("obo-graph-json"!==n)throw new Error(`ontology source file ${JSON.stringify(e)} has type ${n}, which is not yet supported`);return await this.loadOboGraphJson(t),t}catch(e){throw t.close(),await C.deleteDB(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const a of e)t.has(a.id)||(t.set(a.id,!0),n.push(a));return n}async getTermsWithLabelOrSynonym(e,t,n){const a=t?.includeSubclasses??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),s=r.objectStore("nodes"),l=[...await s.index("by-label").getAll(e),...await s.index("by-synonym").getAll(e)];if(a){const e=await this.recurseEdges("by-object",l.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",r);for(const t of e){const e=await s.get(t);e&&l.push(e)}}return l}async getPropertiesByLabel(e,t,n){const a=t?.includeSubProperties??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),s=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},r)).filter((e=>at(e)));if(a){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"subPropertyOf"===e.pred),"sub",r),t=r.objectStore("nodes");for(const n of e){const e=await t.get(n);e&&at(e)&&s.push(e)}}return s}async recurseEdges(e,t,n,a,o){const r=new Set;return await async function t(s){await Promise.all([...s].map((async s=>{const l=(await o.objectStore("edges").index(e).getAll(s)).filter((e=>n(e))).map((e=>e[a]));if(l.length>0){for(const e of l)r.add(e);await t(l)}})))}(t),r.values()}async*expandNodeSet(e,t="is_a",n,a){const o=await this.db,r=a??o.transaction(["edges"]),s=[...e],l=await this.recurseEdges("subclasses"===n?"by-object":"by-subject",s,(e=>e.pred===t),"subclasses"===n?"sub":"obj",r);for(const e of s)yield e;for(const e of l)yield e}expandSubclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"subclasses",n)}expandSuperclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"superclasses",n)}async getClassesThat(e,t,n){const a=await this.db,o=n??a.transaction(["nodes","edges"]),r=await this.getPropertiesByLabel(e,{includeSubProperties:!0},o),s=new Set(r.map((e=>e.id))),l=await async function(e){const t=[];for await(const n of e)t.push(n);return t}(this.expandSuperclasses(t.map((e=>e.id)),"is_a",o)),i=await this.recurseEdges("by-object",l,(e=>s.has(e.pred)),"sub",o),c=this.expandSubclasses(i,"is_a",o),u=[];for await(const e of c){const t=await o.objectStore("nodes").get(e);t&&nt(t)&&!He(t)&&u.push(t)}return u}async getClassesWithoutPropertyLabeled(e,t,n){const a=await 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this.findOntology(e,t)?.dataStore},applyPrefixes:t=>Le(t,e.prefixes),expandPrefixes:t=>function(e,t){for(const[n,a]of t.entries())if(e.startsWith(n))return e.replace(n,a);return e}(t,e.prefixes)}))).actions((e=>({addOntology(t,n,a,o){const r=e.ontologies.push({name:t,version:n,source:a,options:{prefixes:new Map(e.prefixes.entries()),...o}});e.ontologies[r-1].ping()}}))),et=[{displayName:"Label",jsonPath:"$.lbl"},{displayName:"Synonym",jsonPath:"$.meta.synonyms[*].val"},{displayName:"Definition",jsonPath:"$.meta.definition.val"}],tt=n.ConfigurationSchema("OntologyRecord",{name:{type:"string",description:'the full name of the ontology, e.g. "Gene Ontology"',defaultValue:"My Ontology"},version:{type:"string",description:"the ontology's version string",defaultValue:"unversioned"},source:{type:"fileLocation",description:"the download location for the ontology's source 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p&&(T.error=!0,T.helperText=p),re.default.createElement(f.Autocomplete,{style:i,autoComplete:!0,filterSelectedOptions:!0,disableClearable:!0,selectOnFocus:!0,clearOnBlur:!0,handleHomeEndKeys:!0,freeSolo:!0,value:c,options:m??[],onOpen:()=>{d(!0)},onClose:()=>{d(!1)},loading:C,renderInput:s??(e=>re.default.createElement(f.TextField,{...e,...T})),getOptionLabel:e=>"string"==typeof e?e:e.lbl??"",isOptionEqualToValue:(e,t)=>e.lbl===t.lbl,onChange:(e,t)=>{t&&("string"==typeof t?(S(void 0),a(c,t)):t.lbl!==c&&(y(""),S(t),a(c,t.lbl)))}})}function st({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{notify:s}=a,[l,i]=h.useState(String(r.max)),[c,u]=h.useState(String(r.min+1)),[d,m]=h.useState(""),[g,p]=h.useState(""),[y,b]=h.useState(""),S=Number(l)<=Number(c);return re.default.createElement(De,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},re.default.createElement("form",{onSubmit:async function(a){a.preventDefault(),p("");const i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new oe.default).toHexString(),refSeq:r.refSeq,min:Number(c)-1,max:Number(l),type:d},parentFeatureId:r._id});await e.submit(i),s("Feature added successfully","success"),n(),a.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{u(e.target.value)}}),re.default.createElement(f.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:l,onChange:e=>{i(e.target.value)},error:S,helperText:S?'"End" must be greater than "Start"':null}),re.default.createElement(rt,{session:a,ontologyName:"Sequence Ontology",style:{width:170},value:d,filterTerms:nt,fetchValidTerms:async function(e,t,n){const a=await ot(e,t);if(a)return a;b(`Type "${e?.type}" does not have any children in the ontology`)}.bind(null,r),renderInput:e=>re.default.createElement(f.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0,error:Boolean(y),helperText:y}),onChange:(e,t)=>{var n;t&&(n=t,p(""),m(n))}})),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{variant:"contained",type:"submit",disabled:S||!(c&&l&&d)},"Submit"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),g?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},g)):null)}function lt({changeManager:e,handleClose:n,region:a,session:o}){const{notify:r}=o,[s,l]=h.useState(String(a.end)),[i,c]=h.useState(String(a.start+1)),[u,d]=h.useState(""),[m,g]=h.useState(),[p,y]=h.useState(""),b=Number(s)<=Number(i);return re.default.createElement(De,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},re.default.createElement("form",{onSubmit:async function(l){let c;l.preventDefault(),y("");for(const[,e]of o.apolloDataStore.assemblies??new Map)if(e._id===a.assemblyName)for(const[,t]of e.refSeqs??new Map)t.name===a.refName&&(c=t._id);if(!c)return void y("Invalid refseq id");const d=(new oe.default).toHexString(),f=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(i)-1,max:Number(s),type:u,strand:m}});await e.submit(f),r("Feature added successfully","success"),n(),l.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(i),onChange:e=>{c(e.target.value)}}),re.default.createElement(f.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:s,onChange:e=>{l(e.target.value)},error:b,helperText:b?'"End" must be greater than "Start"':null}),re.default.createElement(rt,{session:o,ontologyName:"Sequence Ontology",style:{width:170},value:u,filterTerms:nt,renderInput:e=>re.default.createElement(f.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,y(""),d(n))}}),re.default.createElement(f.FormControl,null,re.default.createElement(f.InputLabel,{id:"demo-simple-select-label"},"Strand"),re.default.createElement(f.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:m?.toString(),onChange:function(e){switch(y(""),Number(e.target.value)){case 1:g(1);break;case-1:g(-1);break;default:g(void 0)}}},re.default.createElement(f.MenuItem,{value:void 0}),re.default.createElement(f.MenuItem,{value:1},"+"),re.default.createElement(f.MenuItem,{value:-1},"-")))),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{variant:"contained",type:"submit",disabled:b||!(i&&s&&u)},"Submit"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),p?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},p)):null)}function it(e,t){const n=(new oe.default).toHexString();t.push(n);const a={};if(e.children)for(const n of Object.values(e.children)){const e=it(n,t);a[e._id]=e}const o="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString();return{...e,refSeq:o,children:e.children&&a,_id:n}}function ct({changeManager:e,handleClose:a,session:o,sourceAssemblyId:r,sourceFeature:s}){const{assemblyManager:l,notify:c}=o,u=l.assemblyList,[d,m]=h.useState(u.find((e=>e.name!==r))?.name),[g,p]=h.useState([]),[y,b]=h.useState(""),[S,w]=h.useState(s.min),[v,C]=h.useState("");function E(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=E(a,t);e.refSeq=y,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),o="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:a,children:e.children&&n,_id:o}}return h.useEffect((()=>{b(""),async function(){if(!d)return void C("No assemblies to copy to");const e=await l.waitForAssembly(d);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const n=[...Object.entries(t)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t??""})));p(n),b(n[0]?._id||"")}().catch((e=>{C(String(e))}))}),[d,l]),re.default.createElement(De,{open:!0,title:"Copy features and annotations",handleClose:a,maxWidth:!1,"data-testid":"copy-feature"},re.default.createElement("form",{onSubmit:async function(n){if(!d)return;n.preventDefault(),C("");const o=s.length,r=await l.waitForAssembly(d);if(!r)return void C(`Assembly not found: ${d}.`);const u=r.getCanonicalRefName(y),f=r.regions?.find((e=>e.refName===u));if(!f)return void C(`RefSeq not found: ${y}.`);const m=S+o;if(m>f.end)return void C(`Feature would extend beyond the bounds of the selected reference sequence. 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assembly"),re.default.createElement(f.Select,{labelId:"label",value:d,onChange:function(e){m(e.target.value)}},u.filter((e=>e.name!==r)).map((e=>re.default.createElement(f.MenuItem,{key:e.name,value:e.name},n.readConfObject(e,"displayName"))))),re.default.createElement(f.DialogContentText,null,"Target reference sequence"),re.default.createElement(f.Select,{labelId:"label",value:y,onChange:function(e){b(e.target.value)}},g.map((e=>re.default.createElement(f.MenuItem,{key:e._id,value:e._id},e.name)))),re.default.createElement(f.DialogContentText,null,"Start position in target reference sequence"),re.default.createElement(f.TextField,{margin:"dense",type:"number",fullWidth:!0,variant:"outlined",value:S,onChange:e=>{w(Number(e.target.value))}})),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{disabled:!d||!y||!S,variant:"contained",type:"submit"},"Submit"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:a},"Cancel"))),v?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},v)):null)}function ut({changeManager:e,handleClose:n,session:a}){const{internetAccounts:o}=i.getRoot(a),[r,s]=h.useState(),[l,c]=h.useState(""),[u,d]=h.useState(!1),[m,g]=h.useState(!1),p=o.filter((e=>"ApolloInternetAccount"===e.type));if(0===p.length)throw new Error("No Apollo internet account found");const[y,b]=h.useState(p[0]),{collaborationServerDriver:S}=a.apolloDataStore,w=S.getAssemblies();return h.useEffect((()=>{w.length>0&&void 0===r&&s(w[0])}),[w,r]),re.default.createElement(De,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},re.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),g(!0),c(""),!r)return void c("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:r.name});await e.submit(o,{internetAccountId:y.internetAccountId}),n(),a.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},p.length>1?re.default.createElement(re.default.Fragment,null,re.default.createElement(f.DialogContentText,null,"Select account"),re.default.createElement(f.Select,{value:y.internetAccountId,onChange:function(e){g(!1);const t=p.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);b(t)},disabled:m&&!l},o.map((e=>re.default.createElement(f.MenuItem,{key:e.id,value:e.internetAccountId},e.name))))):null,re.default.createElement(f.DialogContentText,null,"Select assembly"),re.default.createElement(f.Select,{labelId:"label",value:r?.name??"",onChange:function(e){const t=w.find((t=>t.name===e.target.value));s(t)},disabled:0===w.length},w.map((e=>re.default.createElement(f.MenuItem,{key:e.name,value:e.name},e.displayName??e.name)))),re.default.createElement(f.DialogContentText,null,re.default.createElement("strong",{style:{color:"red"}},"NOTE: All assembly data will be deleted and this operation cannot be undone!")),re.default.createElement(f.FormGroup,null,re.default.createElement(f.FormControlLabel,{control:re.default.createElement(f.Checkbox,{checked:u,onChange:()=>{d(!u)}}),label:"I understand that all assembly data will be deleted"}))),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{disabled:!r||!u,variant:"contained",type:"submit"},"Delete"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),l?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},l)):null)}function dt({changeManager:e,handleClose:n,selectedFeature:a,session:o,setSelectedFeature:r,sourceAssemblyId:s,sourceFeature:l}){const{notify:c}=o,[u,d]=h.useState("");return re.default.createElement(De,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature"},re.default.createElement("form",{onSubmit:async function(o){o.preventDefault(),d(""),a?._id===l._id&&r();const u=new t.DeleteFeatureChange({changedIds:[l._id],typeName:"DeleteFeatureChange",assembly:s,deletedFeature:i.getSnapshot(l),parentFeatureId:l.parent?._id});await e.submit(u),c("Feature deleted successfully","success"),n(),o.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.DialogContentText,null,"Are you sure you want to delete the selected feature?")),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{variant:"contained",type:"submit"},"Yes"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),u?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},u)):null)}function ft({handleClose:e,session:a}){const[o,r]=h.useState(),[s,l]=h.useState(""),{collaborationServerDriver:c,getInternetAccount:u,inMemoryFileDriver:d}=a.apolloDataStore,m=[...c.getAssemblies(),...d.getAssemblies()];return re.default.createElement(De,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3"},re.default.createElement("form",{onSubmit:async function(r){if(r.preventDefault(),l(""),!o)return void l("Must select assembly to download");const{internetAccountConfigId:s}=n.getConf(o,["sequence","metadata"]);s?await async function(e){if(!o)return void l("Must select assembly to download");const t=u(o.configuration.name,e),n=new URL("export/getID",t.baseURL),a=new URLSearchParams({assembly:o.name});n.search=a.toString();const r=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:r}),i=await s(r,{method:"GET"});if(!i.ok){const e=await Ne(i,"Error when exporting ID");return void l(e)}const{exportID:c}=await i.json(),d=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c});d.search=f.toString();const m=d.toString();window.open(m,"_blank")}(s):function(e){if(!o)return void l("Must select assembly to download");const{assemblies:a}=e.apolloDataStore,r=a.get(o.name),s=r?.refSeqs;if(!s)return void l(`No refSeqs found for assembly "${o.name}"`);const c=[{directive:"gff-version",value:"3"}],u=n.getConf(o,["sequence","adapter","features"]);for(const e of u){const{end:t,refName:n,start:a}=e;c.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of s){const{features:n}=e;if(n)for(const[,e]of n)c.push(t.makeGFF3Feature(i.getSnapshot(e)))}for(const e of u){const{refName:t,seq:n}=e;c.push({id:t,description:"",sequence:n})}const d=ee.default.formatSync(c),f=new Blob([d],{type:"text/plain;charset=utf-8"});k.saveAs(f,`${o.displayName??o.name}.gff3`)}(a),e()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.DialogContentText,null,"Select assembly"),re.default.createElement(f.Select,{labelId:"label",value:o?.name??"",onChange:function(e){const 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Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).actions((e=>({initialize:i.flow((function*(t){if("admin"===t){const t=i.getRoot(e);r.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Add Assembly",onClick:e=>{e.queueDialog((t=>[Me,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Delete Assembly",onClick:e=>{e.queueDialog((t=>[ut,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Import Features",onClick:e=>{e.queueDialog((t=>[mt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Ft,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Manage Users",onClick:e=>{e.queueDialog((t=>[ht,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Undo",onClick:e=>{const{apolloDataStore:t}=e,{notify:n}=e;t.changeManager.recentChanges.length>0?t.changeManager.revertLastChange():n("No changes to undo","info")}})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:n}=e,a=new URL("users/locations",n).href,o=e.getFetcher({locationType:"UriLocation",uri:a});yield o(a,{method:"GET"}),window.addEventListener("beforeunload",(()=>{e.postUserLocation([])})),document.addEventListener("visibilitychange",(()=>{if("hidden"===document.visibilityState&&e.postUserLocation([]),"visible"===document.visibilityState){const{session:t}=i.getRoot(e);t.broadcastLocations()}}))}))}))).actions((e=>({afterAttach(){e.setRole(),l.autorun((async t=>{if(Ot)return;const{session:n}=i.getRoot(e);n&&e.role&&(await 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this.regions=a,a}getFeatures(e,t){const{end:a,refName:o,start:r}=e,s=n.readConfObject(this.config,"assemblyId"),l={...e,assemblyName:s};return _.ObservableCreate((async e=>{if(!Wt){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)return void e.error("No Apollo data store found");const n=t.getBackendDriver(s),{seq:i}=await n.getSequence(l);return e.next(new ye.default({id:`${o} ${r}-${a}`,data:{refName:o,start:r,end:a,seq:i}})),void e.complete()}const n=await new Promise(((e,n)=>{const a=setTimeout((()=>{n("timeout")}),2e4),o=q.nanoid(),r=t=>{const{data:n}=t;Gt(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),e(n.sequence))};addEventListener("message",r,t),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:l,messageId:o})}));e.next(new ye.default({id:`${o} ${r}-${a}`,data:{refName:o,start:r,end:a,seq:n}})),e.complete()}))}freeResources(){}}var zt=n.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function Vt(e,t,n,a,o,r){const s=a/o;e.fillStyle="black",e.fillRect(t,n,s,r),s>2&&(e.clearRect(t+1,n+1,s-2,r-2),e.fillStyle="rgba(255,255,255,0.75)",e.fillRect(t+1,n+1,s-2,r-2))}var Jt=S.observer((function(e){const[a,o]=h.useState(),[s,c]=h.useState(),u=h.useRef(null),d=h.useRef(null),m=h.useRef(null),[g,p]=h.useState(!1),[y,b]=h.useState(!0),[S,w]=h.useState(),[v,C]=h.useState(!1),[E,x]=h.useState([]),{bpPerPx:A,displayModel:T,regions:k}=e,{session:N}=T,{collaborators:R}=N;h.useEffect((()=>l.autorun((()=>{x(l.toJS(R))}))),[]);const[D]=k,F=(D.end-D.start)/A,{apolloFeatureUnderMouse:M,apolloRowHeight:I,apolloRowUnderMouse:L,changeManager:q,codonLayout:P,featureLayout:U,features:B,featuresHeight:_,getAssemblyId:j,selectedFeature:O,setApolloFeatureUnderMouse:$,setApolloRowUnderMouse:G,setSelectedFeature:W,showIntronLines:H,showStartCodons:z,showStopCodons:V}=T,J=[...B.values()].map((e=>[...e.values()].map((e=>i.getSnapshot(e))))),X=h.useMemo((()=>{const{internetAccounts:e}=i.getRoot(N),{assemblyName:t}=D,{assemblyManager:a}=r.getSession(T),o=a.get(t);if(!o)throw new Error(`No assembly found with name 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0)},changeManager:q,sourceFeature:s,sourceAssemblyId:e}]))}},"Copy features and annotations"),re.default.createElement(f.MenuItem,{disabled:!g,key:3,value:3,onClick:()=>{if(!s)return;const e=j(D.assemblyName);N.queueDialog((t=>[dt,{session:N,handleClose:()=>{t(),c(void 0)},changeManager:q,sourceFeature:s,sourceAssemblyId:e,selectedFeature:O,setSelectedFeature:W}]))}},"Delete feature")),re.default.createElement("canvas",{ref:u,width:F,height:_,style:{position:"absolute",left:0,top:0}}),re.default.createElement("canvas",{ref:d,width:F,height:_,onMouseLeave:function(){$(),G()},onMouseUp:async function(){if(v){if(S){const e=j(D.assemblyName),{bp:n,edge:a,feature:o}=S;let r;if("end"===a){const a=o._id,s=o.max,l=Math.round(n);r=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[a],featureId:a,oldEnd:s,newEnd:l,assembly:e})}else{const a=o._id,s=o.min,l=Math.round(n);r=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[a],featureId:a,oldStart:s,newStart:l,assembly:e})}await q.submit(r)}}else M&&W(M);w(void 0),C(!1)},onContextMenu:function(e){e.preventDefault(),c(M),o([e.pageX,e.pageY])},style:{position:"absolute",left:0,top:0}}),re.default.createElement("canvas",{ref:m,width:F,height:6*I,style:{position:"absolute",left:0,top:0}}))})),Xt=n.ConfigurationSchema("ApolloSixFrameRenderer",{},{explicitlyTyped:!0});class Yt extends a.RendererType{async renderInClient(e,t){return this.render(t)}async freeResourcesInClient(e,t){return 0}}class Kt extends B.BaseAdapter{get baseURL(){return n.readConfObject(this.config,"baseURL").uri}get trackId(){return n.readConfObject(this.config,"trackId")}get assemblyNames(){return n.readConfObject(this.config,"assemblyNames")}mapBaseResult(e,t,n){return e.map((e=>{const a=t.getCanonicalRefName(e.refSeq);return new be.default({label:n,trackId:this.trackId,locString:`${a}:${e.min+1}..${e.max}`})}))}async searchIndex(e){const t=e.queryString,n=[],a=this.pluginManager?.rootModel?.session;if(!a)return n;const{apolloDataStore:o}=a,{assemblyManager:r}=a;for(const a of this.assemblyNames){const s=o.getBackendDriver(a),l=r.get(a);if(!s||!l)continue;const i=await s.searchFeatures(e.queryString,[a]);n.push(...this.mapBaseResult(i,l,t))}return n}freeResources(){}}var Zt=n.ConfigurationSchema("ApolloTextSearchAdapter",{assemblyNames:{type:"stringArray",defaultValue:[],description:"List of assemblies covered by text search adapter"},trackId:{type:"string",defaultValue:""},baseURL:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}}},{explicitlyTyped:!0,explicitIdentifier:"textSearchAdapterId"});const Qt=n.ConfigurationSchema("ApolloPlugin",{ontologies:i.types.array(tt),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"}});function en(e){if("LinearPileupDisplay"!==e.name)return e;const{stateModel:n}=e,a=n.views((e=>({getFirstRegion:()=>r.getContainingView(e).dynamicBlocks.contentBlocks[0],getAssembly(){const t=e.getFirstRegion(),n=r.getSession(e),{assemblyManager:a}=n,{assemblyName:o}=t,s=a.get(o);if(!s)throw new Error(`Could not find assembly named ${o}`);return s},getRefSeqId(t){const n=e.getFirstRegion(),{refName:a}=n,{refNameAliases:o}=t;if(!o)throw new Error(`Could not find aliases for ${t.name}`);const r=[...Object.entries(o)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t??""}))),s=r.find((e=>e.name===a))?._id;if(!s)throw new Error(`Could not find refSeqId named ${a}`);return s},createFeature(){const t=e.contextMenuFeature,n=e.getAssembly(),a=e.getRefSeqId(n),o=(t.get("CIGAR").toUpperCase().match(/\d+\D/g)??[]).map((e=>[(/\D/.exec(e)??[])[0],Number.parseInt(e,10)]));let r=0;const s=t.get("start");let l;const i=[];for(const[e,t]of o)"M"===e||"="===e?void 0===l&&(l=r+s):"N"===e&&void 0!==l&&(i.push({start:l,end:r+l}),l=void 0),"I"!==e&&(r+=t);void 0!==l&&i.push({start:l,end:r+s});const c={_id:oe.default().toHexString(),refSeq:a,min:t.get("start"),max:t.get("end"),type:"mRNA",strand:t.get("strand")};if(0===i.length)return c;c.children={};const[u]=i,d={_id:oe.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"CDS",strand:t.get("strand")};if(c.children[d._id]=d,1===i.length){const e={_id:oe.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"exon",strand:t.get("strand")};return c.children[e._id]=e,c}for(const e of i){d.min=Math.min(d.min,e.start),d.max=Math.max(d.max,e.end);const{end:n,start:o}=e,r={_id:oe.default().toHexString(),refSeq:a,min:o,max:n,type:"exon",strand:t.get("strand")};c.children[r._id]=r}return c},async onPileupFeatureContext(){const n=e.createFeature(),a=e.getAssembly(),o=new t.AddFeatureChange({changedIds:[n._id],typeName:"AddFeatureChange",assembly:a.name,addedFeature:n}),s=r.getSession(e);await s.apolloDataStore.changeManager.submit(o),s.notify("Annotation added 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Ontology"})]]),an=["ID","Name","Alias","Target","Gap","Derives_from","Note","Dbxref","Ontology","Is_Circular"],on=w.makeStyles()((e=>({newAttributePaper:{padding:e.spacing(2)},attributeName:{background:e.palette.secondary.main,color:e.palette.secondary.contrastText,padding:e.spacing(1)}})));function rn(e){const{onChange:t,value:n}=e;return re.default.createElement(tn,{value:n,onChangeCommitted:e=>{t(e.split(","))},variant:"outlined",fullWidth:!0,helperText:"Separate multiple values for the attribute with commas"})}const sn=S.observer((function({assembly:e,editable:n,feature:a,session:o}){const[r,s]=h.useState(""),[l,c]=h.useState(!1),{classes:u}=on(),[d,m]=h.useState(""),g=Object.fromEntries([...a.attributes.entries()].map((([e,t])=>{if(e.startsWith("gff_")){const n=e.slice(4);return[n.charAt(0).toUpperCase()+n.slice(1),i.getSnapshot(t)]}return"_id"===e?["ID",i.getSnapshot(t)]:[e,i.getSnapshot(t)]}))),{notify:p}=o,{changeManager:y}=o.apolloDataStore;async function b(n,o){s("");const r={};if(g){const e=Object.entries({...g,[n]:o});for(const[t,n]of e)if(n&&"parent"!==t.toLowerCase())if([...nn.keys()].includes(t))r[t]=n;else switch(t){case"ID":r._id=n;break;case"Name":r.gff_name=n;break;case"Alias":r.gff_alias=n;break;case"Target":r.gff_target=n;break;case"Gap":r.gff_gap=n;break;case"Derives_from":r.gff_derives_from=n;break;case"Note":r.gff_note=n;break;case"Dbxref":r.gff_dbxref=n;break;case"Ontology_term":r.gff_ontology_term=n;break;case"Is_circular":r.gff_is_circular=n;break;default:r[t.toLowerCase()]=n}}const l=new t.FeatureAttributeChange({changedIds:[a._id],typeName:"FeatureAttributeChange",assembly:e,featureId:a._id,attributes:r});await y.submit(l),p("Feature attributes modified successfully","success")}return re.default.createElement(re.default.Fragment,null,re.default.createElement(f.Typography,{variant:"h5"},"Attributes"),re.default.createElement(f.Grid,{container:!0,direction:"column",spacing:1},Object.entries(g).map((([e,t])=>{if(""===e)return null;const a=nn.get(e)??rn;return re.default.createElement(f.Grid,{container:!0,item:!0,spacing:3,alignItems:"center",key:e},re.default.createElement(f.Grid,{item:!0,xs:"auto"},re.default.createElement(f.Paper,{variant:"outlined",className:u.attributeName},re.default.createElement(f.Typography,null,e))),re.default.createElement(f.Grid,{item:!0,flexGrow:1},re.default.createElement(a,{session:o,value:t,onChange:t=>b(e,t)})),re.default.createElement(f.Grid,{item:!0,xs:1},re.default.createElement(f.IconButton,{"aria-label":"delete",size:"medium",disabled:!n,onClick:()=>b(e)},re.default.createElement(fe.default,{fontSize:"medium",key:e}))))})),re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.Button,{color:"primary",variant:"contained",disabled:l||!n,onClick:()=>{c(!0)}},"Add new")),l?re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.Paper,{elevation:8,className:u.newAttributePaper},re.default.createElement(f.Grid,{container:!0,direction:"column"},re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.FormControl,null,re.default.createElement(f.FormLabel,{id:"attribute-radio-button-group"},"Select attribute type"),re.default.createElement(f.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:"custom",name:"radio-buttons-group",onChange:function(e,t){"custom"===t?m(""):nn.has(t)?m(t):s("Unknown attribute 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re.default.createElement("div",{onMouseDown:e=>{e.stopPropagation(),globalThis.addEventListener("mousemove",n),globalThis.addEventListener("mouseup",a),globalThis.addEventListener("mouseleave",a)},onClick:e=>{e.stopPropagation(),e.preventDefault()},className:t.resizeHandle})},Na=S.observer((function({onClick:e,onResize:t,open:n,title:a}){const{classes:o}=Ta();return re.default.createElement("div",{className:o.accordionRoot},n&&t?re.default.createElement(ka,{onResize:t}):null,re.default.createElement("div",{className:o.accordionControl,onClick:e},re.default.createElement(n?ve.default:Ce.default,{className:o.expandIcon}),a?re.default.createElement(f.Typography,{className:o.title,variant:"caption",component:"span"},a):null))})),Ra=S.observer((function({model:e,...t}){const n=r.getSession(e),{ontologyManager:a}=n.apolloDataStore,{featureTypeOntology:o}=a,s=o?.dataStore,{classes:l}=Ta(),{detailsHeight:i,graphical:c,height:u,isShown:d,selectedFeature:m,table:g,tabularEditor:p,toggleShown:y}=e,b=h.useRef(null);h.useEffect((()=>{!function(e,t){const{apolloRowHeight:n,selectedFeature:a}=e;if(t.current&&a){const o=e.getFeatureLayoutPosition(a);o&&t.current.scroll({top:(o.layoutRow+o.featureRow)*n,behavior:"smooth"})}}(e,b)}),[e,m]);const S=t=>{e.setDetailsHeight(i-t)};if(!s)return re.default.createElement("div",{className:l.alertContainer},re.default.createElement(f.Alert,{severity:"error"},"Could not load feature type ontology."));if(c&&g){const n=p.isShown?i:0,a=d?u-i-24:0;return 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n||(n=r.getSession(e).addWidget("JobsListWidget","JobsList")),n}}))).actions((e=>({update(t,n,a){e.jobStatusWidget.updateJobStatusMessage(t,n),a&&e.jobStatusWidget.updateJobProgressPct(t,a)},abortJob(t,n){const a=r.getSession(e);if(r.isSessionModelWithWidgets(a)){a.showWidget(e.jobStatusWidget),e.jobStatusWidget.updateJobStatusMessage(t,n??"Aborted unexpectedly");const o=e.jobStatusWidget.jobs.findIndex((e=>e.name===t));e.jobStatusWidget.addAbortedJob({...e.jobStatusWidget.jobs[o]}),e.jobStatusWidget.removeJob(t),a.notify("Job aborted","info")}},runJob(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.removeJob(t.name),e.jobStatusWidget.addFinishedJob({name:t.name,statusMessage:"All operations successful",progressPct:100,cancelCallback:t.cancelCallback}))}})));class Fa{clientStore;constructor(e){this.clientStore=e}}class Ma{dataStore;constructor(e){this.dataStore=e}recentChanges=[];async submit(n,a={}){const{addToRecents:o=!0,submitToBackend:s=!0,updateJobsManager:l=!1}=a,i=r.getSession(this.dataStore),c=new AbortController,{jobsManager:u}=r.getSession(this.dataStore),d={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort()}};l&&u.runJob(d);const f=await t.validationRegistry.frontendPreValidate(n);if(!f.ok){const e=`Pre-validation failed: "${f.resultsMessages}"`;return l&&u.abortJob(d.name,e),void i.notify(e,"error")}try{await n.execute(this.dataStore)}catch(e){return l&&u.abortJob(d.name,String(e)),console.error(e),void i.notify(String(e),"error")}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.revert(n),s){l&&u.update(d.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:o}=this.dataStore,r=e.isAssemblySpecificChange(n)?o(n.assembly):t;let s;try{s=await r.submitChange(n,a)}catch(e){return l&&u.abortJob(d.name,String(e)),console.error(e),i.notify(String(e),"error"),void await this.revert(n,!1)}if(!s.ok){const e=`Post-validation failed: "${f.resultsMessages}"`;return l&&u.abortJob(d.name,e),i.notify(e,"error"),void await this.revert(n,!1)}n.notification&&i.notify(n.notification,"success")}o&&this.recentChanges.push(n),l&&u.done(d)}async revert(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async revertLastChange(){const e=this.recentChanges.pop();if(e)return this.revert(e);r.getSession(this.dataStore).notify("No changes to undo!","warning")}}class Ia extends Fa{inFlight=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:a}=n,o=new URL("features/searchFeatures",a),r=new URLSearchParams({assemblies:t.join(","),term:e});o.search=r.toString();const s=o.toString(),l=await this.fetch(n,s);if(!l.ok){const e=await Ne(l,"searchFeatures failed");throw new Error(e)}return l.json()}async getFeatures(e){const{assemblyName:t,end:a,refName:o,start:s}=e,{assemblyManager:l}=r.getSession(this.clientStore),i=l.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=n.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(s),end:String(a)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await Ne(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),s=`${t}-${n}`,l=new Ma(this.clientStore);o.hasListeners(s)||o.on(s,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===s){const n=e.Change.fromJSON(t.changeInfo);await l.submit(n,{submitToBackend:!1})}}))}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,a=this.inFlight.get(t),{assemblyName:o,end:s,refName:l,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=n.getConf(u,["sequence","metadata"]),f=d[l];if(!f)throw new Error(`Could not find refSeq "${l}"`);if(a)return{seq:await a,refSeq:f};let m=this.clientStore.assemblies.get(o);m||(m=this.clientStore.addAssembly(o));let g=m.refSeqs.get(f);g||(g=m.addRefSeq(f,l));const p=g.getSequence(i,s);if(p.length===s-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(s)});b.search=S.toString();const w=b.toString(),v=this.getSeqFromServer(h,w,g,i,s);this.inFlight.set(t,v);const C=await v;return this.checkSocket(o,l,h),this.inFlight.delete(t),{seq:C,refSeq:f}}async getSeqFromServer(e,t,n,a,o){const r=await this.fetch(e,t);if(!r.ok){let e;try{e=await r.text()}catch{e=""}throw new Error(`getSequence failed: ${r.status} (${r.statusText})${e?` (${e})`:""}`)}const s=await r.text();return n.addSequence({sequence:s,start:a,stop:o}),s}async getRefNameAliases(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),s=new URLSearchParams({assembly:e});o.search=s.toString();const l=o.toString(),i=await this.fetch(n,l);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),s=new URLSearchParams({assembly:e});o.search=s.toString();const l=o.toString(),i=await this.fetch(n,l);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRegions failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(e){const{assemblyManager:t}=r.getSession(this.clientStore);return t.assemblies.filter((t=>{const a=n.getConf(t,["sequence","metadata"]);return!(!(a&&a.apollo&&a.internetAccountConfigId)||e&&a.internetAccountConfigId!==e)}))}async submitChange(e,n={}){const{internetAccountId:a}=n,o=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,a),{baseURL:r}=o,s=new URL("changes",r).href,l=await this.fetch(o,s,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!l.ok){const e=await Ne(l,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return l.ok||(i.ok=!1),i}}class La extends Fa{async getFeatures(){return[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=this.clientStore.assemblies.get(t);if(!r)return{seq:"",refSeq:a};const s=r.refSeqs.get(a);return s?{seq:s.getSequence(o,n),refSeq:a}:{seq:"",refSeq:a}}async getRefNameAliases(e){const t=this.clientStore.assemblies.get(e),n=[];if(!t)return n;for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getRegions(e){const t=this.clientStore.assemblies.get(e);if(!t)return[];const n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=n.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class qa extends Fa{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),a=t.get(e);if(!a)throw new Error(`Assembly ${e} not found`);const{file:o}=n.getConf(a,["sequence","metadata"]),s=require("node:fs");return Te(e,await s.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=(await this.getAssembly(t)).refSeqs.get(a);if(!r)throw new Error(`refSeq ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=n.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(a){if(!e.isAssemblySpecificChange(a))throw new Error(`Cannot use this type of change with local file: "${a.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),s=o.get(a.assembly);if(!s)throw new Error(`Could not find assembly with name "${a.assembly}"`);const{file:l}=n.getConf(s,["sequence","metadata"]),c=this.clientStore.assemblies.get(a.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${a.assembly}"`);const u=new Set(...c.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await ke(c);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.makeGFF3Feature(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=ee.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(l,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function Pa(e,a){const o=new AbortController,{signal:s}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",$.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map($.ApolloAssembly),checkResults:i.types.map($.CheckResult),ontologyManager:i.types.optional(Qe,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):i.getParentOfType(n,$.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)}}))).volatile((e=>({changeManager:new Ma(e),collaborationServerDriver:new Ia(e),inMemoryFileDriver:new La(e),desktopFileDriver:r.isElectron?new qa(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,l.autorun((()=>{const{ontologyManager:t,pluginConfiguration:a}=e,o=a.ontologies;for(const e of 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config id ${a}`);return l}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:s}=n;let l=e.assemblies.get(r);l||(l=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=l.refSeqs.get(i.refSeq);c||(c=l.refSeqs.put({_id:i.refSeq,name:s,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:s,refName:l,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:l,sequence:[]})),u.addSequence({start:i,stop:s,sequence:o})}}))})))}(c),d=a.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(Da,{})}).extend((()=>{const e=l.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,a){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations 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n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).actions((e=>({afterCreate:i.flow((function*(){const t=i.getSnapshot(e),{id:n,name:a}=t;i.applySnapshot(e,{name:a,id:n});const{internetAccounts:o,jbrowse:r}=i.getRoot(e);l.autorun((()=>{const t=[];for(const n of e.views){if("LinearGenomeView"!==n.type)return;const e=n;if(e.initialized){const{dynamicBlocks:n}=e;n.forEach((e=>{if(void 0!==e.regionNumber){const{assemblyName:n,end:a,refName:o,start:r}=e;t.push({assemblyName:n,refName:o,start:r,end:a})}}))}}if(0===t.length){for(const e of o)"baseURL"in e&&e.postUserLocation([]);return}const n=[];for(const e of o)if("baseURL"in e){for(const e of t)n.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(n)}}),{name:"ApolloSession"});for(const n of o){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:a}=n,o=new URL("jbrowse/config.json",a).href,l=n.getFetcher({locationType:"UriLocation",uri:o});let c,u;try{c=yield l(o,{signal:s})}catch(e){console.error(e);continue}if(c.ok){try{u=yield c.json()}catch(e){console.error(e);continue}i.applySnapshot(r,u),i.applySnapshot(e,t)}else{const e=yield Ne(c,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const a=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return a?.(o);const r=n.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...a?.(o)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),s=i.getSnapshot(a);let l;l=t.filterJBrowseConfig(s),0===Object.keys(l).length&&(l=void 0);const c={...i.getSnapshot(o),trackId:r.slice(0,r.length-13)};for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:l,newJBrowseConfig:{...l,tracks:l?.tracks&&[...l.tracks,c]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(c)},icon:xe.default}]:[...a?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),s=i.getSnapshot(a);let l;l=t.filterJBrowseConfig(s),0===Object.keys(l).length&&(l=void 0);const c=l?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:l,newJBrowseConfig:{...l,tracks:c}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:xe.default}]}}}));return i.types.snapshotProcessor(d,{postProcessor(e){e.apolloSelectedFeature=void 0;const t=Object.fromEntries(Object.entries(e.apolloDataStore.assemblies).filter((([,e])=>"InMemoryFileDriver"===e.backendDriverType)));return e.apolloDataStore={typeName:"Client",assemblies:t,checkResults:{}},e}})}const Ua={0:2,1:1,2:0},Ba={3:0,4:1,5:2};function _a(e,t){const a=e.getPlugin("LinearGenomeViewPlugin"),{BaseLinearDisplay:o}=a.exports;return o.named("SixFrameFeatureDisplay").props({type:i.types.literal("SixFrameFeatureDisplay"),configuration:n.ConfigurationReference(t),apolloRowHeight:20,detailsMinHeight:200,showStartCodons:!1,showStopCodons:!0,showIntronLines:!0}).volatile((()=>({apolloFeatureUnderMouse:void 0,apolloRowUnderMouse:void 0}))).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...G.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get regions(){let t;try{({blockDefinitions:t}=e)}catch{return[]}return t.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))},regionCannotBeRendered(){const t=r.getContainingView(e);if(t&&t.bpPerPx>=200)return"Zoom in to see annotations"},get session(){return r.getSession(e)}}))).actions((e=>{let t=[];return{afterAttach(){i.addDisposer(e,l.autorun((()=>{const n=r.getSession(e);if(r.getContainingView(e).initialized){if(e.regionCannotBeRendered())return;const a=[],o=[];for(const n of e.blockDefinitions.contentBlocks)a.push(n.key),t.includes(n.key)||o.push(n);n.apolloDataStore.loadFeatures(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),n.apolloDataStore.loadRefSeq(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),t=a}}),{name:"SixFrameFeatureDisplay"}))}}})).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get changeManager(){return r.getSession(e).apolloDataStore.changeManager},get sequence(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName),r=o?.getSequence(e.start,e.end);a.set(e.start,r??"")}return a},get features(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName);let r=a.get(e.refName);r||(r=new Map,a.set(e.refName,r));for(const[t,n]of o?.features.entries()??new Map)e.start<n.end&&e.end>n.start&&r.set(t,n)}return a},get featuresMinMax(){const e={};for(const[t,n]of this.features||[]){let a,o;for(const[,e]of n)void 0===a&&({min:a}=e),void 0===o&&({max:o}=e),e.min<a&&({min:a}=e),e.max>o&&({max:o}=e);void 0!==a&&void 0!==o&&(e[t]=[a,o])}return e},get codonLayout(){const e=new Map;let t="",n=0;for(const[e,a]of this.sequence||[])a&&(t||(n=e),t+=a);for(let a=0;a<6;a++){const o=[],s=[],l=a in Ba;let i,c,u;l?(i=(t.length+n)%3,c=(Ba[a]+i+3)%3,u=r.reverse(t).slice(c)):(i=3-n%3,c=(Ua[a]+i+3)%3,u=t.slice(c));for(let e=0;e<u.length;e+=3){const t=u.slice(e,e+3),a=l?r.reverse(r.revcom(t)):t,i=l?n+u.length-(3+e):n+e+c;r.defaultStarts.includes(a.toUpperCase())?o.push(i):r.defaultStops.includes(a.toUpperCase())&&s.push(i)}e.set(a,{starts:o,stops:s})}return e},get featureLayout(){const e=new Map;for(const[t,n]of this.features||[]){if(!n)continue;const a=this.featuresMinMax[t];if(!a)continue;const[o,r]=a,s=[],l=6;for(let t=0;t<l;t++){const t=s.length;s[t]=Array.from({length:r-o}),e.set(t,[])}for(const t of[...n.values()].sort(((e,t)=>{const{max:n,min:a}=e,{max:o,min:r}=t;return a-r||n-o})))for(const[,n]of t.children??new Map)if("mRNA"===n.type)for(const[,a]of n.children||new Map){let o;if("CDS"===a.type){let r;a.discontinuousLocations.length>0?({discontinuousLocations:r}=a):r=[a];for(const a of r){const r=a.start+3,s=a.end-3;for(const[l,{stops:i}]of this.codonLayout)if((l<3&&1===t.strand||l>=3&&-1===t.strand)&&0===i.filter((e=>e>=r&&e<=s)).length){o=l;const t=e.get(o);t?.push([n.featureId,a]);break}}}}}return e},getAssemblyId(t){const{assemblyManager:n}=r.getSession(e),a=n.get(t);if(!a)throw new Error(`Could not find assembly named ${t}`);return a.name},get selectedFeature(){return r.getSession(e).apolloSelectedFeature},get setSelectedFeature(){return r.getSession(e).apolloSetSelectedFeature}}))).actions((e=>({setSelectedFeature(t){r.getSession(e).apolloSetSelectedFeature(t)},setApolloFeatureUnderMouse(t){e.apolloFeatureUnderMouse=t},setApolloRowUnderMouse(t){e.apolloRowUnderMouse=t},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleShowIntronLines(){e.showIntronLines=!e.showIntronLines}}))).views((e=>({get highestRow(){return 0===e.featureLayout.size?0:Math.max(...e.featureLayout.keys())},get featuresHeight(){return(this.highestRow+1)*e.apolloRowHeight},get detailsHeight(){return Math.max(e.detailsMinHeight,e.height-this.featuresHeight)},trackMenuItems:()=>[{label:"Show start codons",type:"checkbox",checked:e.showStartCodons,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:e.showStopCodons,onClick:()=>{e.toggleShowStopCodons()}},{label:"Show intron lines",type:"checkbox",checked:e.showIntronLines,onClick:()=>{e.toggleShowIntronLines()}}]})))}var ja=n.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});const Oa="undefined"==typeof sessionStorage;class $a extends B.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=n.readConfObject(this.config,"assemblyId");if(!Oa){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);return await n.getRefNameAliases(e)}const t=await new Promise(((t,n)=>{const a=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=q.nanoid(),r=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in e})(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),t(n.refNameAliases))};addEventListener("message",r),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:o})}));return this.refNameAliases=t,t}freeResources(){}}const Ga="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Wa=new t.CDSCheck;e.checkRegistry.registerCheck(Wa.name,Wa),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends Z.default{name="ApolloPlugin";version="0.2.1";configurationSchema=Qt;install(e){!function(e){e.addAdapterType((()=>new he.default({name:"ApolloSequenceAdapter",configSchema:zt,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Ht})))}(e),function(e){e.addAdapterType((()=>new he.default({name:"ApolloRefNameAliasAdapter",configSchema:ja,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:$a})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:Zt,AdapterClass:Kt,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new a.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:gn,ReactComponent:mn})})),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloTranscriptDetails",{});return new a.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:pn,ReactComponent:vn})})),e.addTrackType((()=>{const t=n.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a.TrackType({name:"ApolloTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new a.InternetAccountType({name:"ApolloInternetAccount",configSchema:Ae,stateModel:$t(Ae)}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloDisplay",configSchema:Cn,stateModel:Ca(0,Cn),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Ra}))),e.addDisplayType((()=>{const t=function(e){const t=e.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=t.exports;return n.ConfigurationSchema("SixFrameFeatureDisplay",{renderer:Xt,height:{type:"number",defaultValue:120}},{baseConfiguration:a,explicitlyTyped:!0})}(e),o=function(e){const t=e.getPlugin("LinearGenomeViewPlugin");if(!t)throw new Error("LinearGenomeView plugin not found");const{BaseLinearDisplayComponent:n}=t.exports;return S.observer((function({model:e,...t}){const{classes:a}=Ta(),{height:o,selectedFeature:r}=e;let{detailsHeight:s}=e;return r||(s=0),re.default.createElement("div",{style:{height:e.height}},re.default.createElement("div",{className:a.shading,style:{height:o-s}},re.default.createElement(n,{model:e,...t})),re.default.createElement("div",{className:"testTrackLines"},re.default.createElement(Aa,{model:e})))}))}(e);return new a.DisplayType({name:"SixFrameFeatureDisplay",configSchema:t,stateModel:_a(e,t),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((()=>new Yt({name:"ApolloSixFrameRenderer",ReactComponent:Jt,configSchema:Xt,pluginManager:e}))),e.addToExtensionPoint("Core-extendSession",Pa.bind(this,e)),e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearGenomeView"===e.name){const{stateModel:t}=e,n=t.views((e=>{const t=e.rubberBandMenuItems;return{rubberBandMenuItems:()=>[...t(),{label:"Add new feature",icon:Q.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[lt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",en),Ga||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t&&t.on?(t.on("apollo",(async n=>{if("object"!=typeof(a=n)||null===a||!("apollo"in a)||!0!==a.apollo)return;var a;const{apollo:o,messageId:r,method:s}=n;switch(s){case"getSequence":{const{region:a}=n,{assemblyName:s}=a,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const i=l.getBackendDriver(s),{seq:c}=await i.getSequence(a);t.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=n,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a),i=await l.getRegions(a);t.workers[0].postMessage({apollo:o,messageId:r,regions:i});break}case"getRefNameAliases":{const{assembly:a}=n,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a),i=await l.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[pt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Nt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[Tt,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[Mt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Log out",onClick:e=>{e.queueDialog((t=>[gt,{session:e,handleClose:()=>{t()}}]))}}))}};
+"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var 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Y(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}function K(e){if(e&&e.__esModule)return e;var t=Object.create(null);return e&&Object.keys(e).forEach((function(n){if("default"!==n){var a=Object.getOwnPropertyDescriptor(e,n);Object.defineProperty(t,n,a.get?a:{enumerable:!0,get:function(){return e[n]}})}})),t.default=e,t}var Z=Y(o),Q=Y(s),ee=Y(u),te=Y(d),ne=Y(m),ae=Y(g),oe=Y(p),re=Y(h),se=K(h),le=Y(b),ie=Y(x),ce=Y(T),ue=Y(N),de=Y(R),fe=Y(D),me=Y(I),ge=Y(L),pe=Y(P),he=Y(U),ye=Y(j),be=Y(O),Se=Y(W),we=Y(H),ve=Y(z),Ce=Y(V),Ee=Y(J),xe=Y(X);const Ae=n.ConfigurationSchema("ApolloInternetAccount",{baseURL:{description:"Location of Apollo server",type:"string",defaultValue:""},tokenType:{description:"A custom name for a token to include in the header",type:"string",defaultValue:"Bearer"}},{baseConfiguration:a.BaseInternetAccountConfig,explicitlyTyped:!0});async function Te(e,n,a){const 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l)E.checkAbortSignal(n),i.push(...$e(this.textIndexFields,e,t,r,this.prefixes));return i.sort(((e,t)=>t.score-e.score)),i.slice(0,this.options.maxSearchResults??this.DEFAULT_MAX_SEARCH_RESULTS)}function $e(e,t,n,a,o){const r=[...n].sort().map((e=>a[e])),s=r.map((e=>{const t=e.replaceAll(/[$()*+./?[\\\]^{|}-]/g,String.raw`\$&`);return new RegExp(`\\b${t}`,"gi")}));let l=[],i=0;for(const[n,r]of e.entries()){const c=new Set,u=e.length-n-1,d=[..._e(Pe(t,r.jsonPath,o))];for(const e of d){let n=0;const o=[];for(const[t,r]of s.entries())for(const s of e.matchAll(r)){n+=1+1*u,c.add(t);const r=s.index,l=a[t];void 0!==r&&(n+=.01*l.length,n+=l.length/e.length*100*.05,o.push({wordIndex:t,position:r}))}n+=100*c.size,i<n&&(i=n),o.sort(((e,t)=>e.position-t.position)),o.length>0&&l.push({term:t,field:r,str:e,score:n,wordMatches:o})}}l=l.filter((e=>e.score===i));for(const e of l){const{wordMatches:t}=e;for(let n=0;n<t.length-1;n++){const 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t=a.objectStore("nodes");t.createIndex("by-label","lbl"),t.createIndex("by-type","type"),t.createIndex("by-synonym",["meta","synonyms","val"]),t.createIndex("full-text-words","fullTextWords",{multiEntry:!0})}if(!e.objectStoreNames.contains("edges")){e.createObjectStore("edges",{autoIncrement:!0});const t=a.objectStore("edges");t.createIndex("by-subject","sub"),t.createIndex("by-object","obj"),t.createIndex("by-predicate","pred")}}})}function Ve(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function Je(e){const t=Date.now();let n;try{n=JSON.parse(await A.openLocation(this.sourceLocation).readFile("utf8"))}catch{throw new Error("Error in loading ontology")}const a=Date.now(),[o,...r]=n.graphs??[];if(o){if(r.length>0)throw new Error("multiple graphs not supported");try{const n=e.transaction(["meta","nodes","edges"],"readwrite");await n.objectStore("meta").clear(),await n.objectStore("nodes").clear(),await n.objectStore("edges").clear();const 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this.recurseEdges("subclasses"===n?"by-object":"by-subject",s,(e=>e.pred===t),"subclasses"===n?"sub":"obj",r);for(const e of s)yield e;for(const e of l)yield e}expandSubclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"subclasses",n)}expandSuperclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"superclasses",n)}async getClassesThat(e,t,n){const a=await this.db,o=n??a.transaction(["nodes","edges"]),r=await this.getPropertiesByLabel(e,{includeSubProperties:!0},o),s=new Set(r.map((e=>e.id))),l=await async function(e){const t=[];for await(const n of e)t.push(n);return t}(this.expandSuperclasses(t.map((e=>e.id)),"is_a",o)),i=await this.recurseEdges("by-object",l,(e=>s.has(e.pred)),"sub",o),c=this.expandSubclasses(i,"is_a",o),u=[];for await(const e of c){const t=await o.objectStore("nodes").get(e);t&&nt(t)&&!He(t)&&u.push(t)}return u}async getClassesWithoutPropertyLabeled(e,t,n){const a=await 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this.findOntology(e,t)?.dataStore},applyPrefixes:t=>Le(t,e.prefixes),expandPrefixes:t=>function(e,t){for(const[n,a]of t.entries())if(e.startsWith(String(n)))return e.replace(String(n),a);return e}(t,e.prefixes)}))).actions((e=>({addOntology(t,n,a,o){const r=e.ontologies.push({name:t,version:n,source:a,options:{prefixes:new Map(e.prefixes.entries()),...o}});e.ontologies[r-1].ping()}}))),et=[{displayName:"Label",jsonPath:"$.lbl"},{displayName:"Synonym",jsonPath:"$.meta.synonyms[*].val"},{displayName:"Definition",jsonPath:"$.meta.definition.val"}],tt=n.ConfigurationSchema("OntologyRecord",{name:{type:"string",description:'the full name of the ontology, e.g. "Gene Ontology"',defaultValue:"My Ontology"},version:{type:"string",description:"the ontology's version string",defaultValue:"unversioned"},source:{type:"fileLocation",description:"the download location for the ontology's source 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p&&(T.error=!0,T.helperText=p),re.default.createElement(f.Autocomplete,{style:i,autoComplete:!0,filterSelectedOptions:!0,disableClearable:!0,selectOnFocus:!0,clearOnBlur:!0,handleHomeEndKeys:!0,freeSolo:!0,value:c,options:m??[],onOpen:()=>{d(!0)},onClose:()=>{d(!1)},loading:C,renderInput:s??(e=>re.default.createElement(f.TextField,{...e,...T})),getOptionLabel:e=>"string"==typeof e?e:e.lbl??"",isOptionEqualToValue:(e,t)=>e.lbl===t.lbl,onChange:(e,t)=>{t&&("string"==typeof t?(S(void 0),a(c,t)):t.lbl!==c&&(y(""),S(t),a(c,t.lbl)))}})}function st({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{notify:s}=a,[l,i]=h.useState(String(r.max)),[c,u]=h.useState(String(r.min+1)),[d,m]=h.useState(""),[g,p]=h.useState(""),[y,b]=h.useState(""),S=Number(l)<=Number(c);return re.default.createElement(De,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},re.default.createElement("form",{onSubmit:async function(a){a.preventDefault(),p("");const i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new oe.default).toHexString(),refSeq:r.refSeq,min:Number(c)-1,max:Number(l),type:d},parentFeatureId:r._id});await e.submit(i),s("Feature added successfully","success"),n(),a.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{u(e.target.value)}}),re.default.createElement(f.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:l,onChange:e=>{i(e.target.value)},error:S,helperText:S?'"End" must be greater than "Start"':null}),re.default.createElement(rt,{session:a,ontologyName:"Sequence Ontology",style:{width:170},value:d,filterTerms:nt,fetchValidTerms:async function(e,t,n){const a=await 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n;t&&(n=t,y(""),d(n))}}),re.default.createElement(f.FormControl,null,re.default.createElement(f.InputLabel,{id:"demo-simple-select-label"},"Strand"),re.default.createElement(f.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:m?.toString(),onChange:function(e){switch(y(""),Number(e.target.value)){case 1:g(1);break;case-1:g(-1);break;default:g(void 0)}}},re.default.createElement(f.MenuItem,{value:void 0}),re.default.createElement(f.MenuItem,{value:1},"+"),re.default.createElement(f.MenuItem,{value:-1},"-")))),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{variant:"contained",type:"submit",disabled:b||!(i&&s&&u)},"Submit"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),p?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},p)):null)}function it(e,t){const n=(new oe.default).toHexString();t.push(n);const a={};if(e.children)for(const n of Object.values(e.children)){const e=it(n,t);a[e._id]=e}const o="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString();return{...e,refSeq:o,children:e.children&&a,_id:n}}function ct({changeManager:e,handleClose:a,session:o,sourceAssemblyId:r,sourceFeature:s}){const{assemblyManager:l,notify:c}=o,u=l.assemblyList,[d,m]=h.useState(u.find((e=>e.name!==r))?.name),[g,p]=h.useState([]),[y,b]=h.useState(""),[S,w]=h.useState(s.min),[v,C]=h.useState("");function E(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=E(a,t);e.refSeq=y,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),o="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:a,children:e.children&&n,_id:o}}return h.useEffect((()=>{b(""),async function(){if(!d)return void C("No assemblies to copy to");const e=await l.waitForAssembly(d);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const 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0===r&&s(w[0])}),[w,r]),re.default.createElement(De,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},re.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),g(!0),c(""),!r)return void c("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:r.name});await e.submit(o,{internetAccountId:y.internetAccountId}),n(),a.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},p.length>1?re.default.createElement(re.default.Fragment,null,re.default.createElement(f.DialogContentText,null,"Select account"),re.default.createElement(f.Select,{value:y.internetAccountId,onChange:function(e){g(!1);const t=p.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID 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deleted"}))),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{disabled:!r||!u,variant:"contained",type:"submit"},"Delete"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),l?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},l)):null)}function dt({changeManager:e,handleClose:n,selectedFeature:a,session:o,setSelectedFeature:r,sourceAssemblyId:s,sourceFeature:l}){const{notify:c}=o,[u,d]=h.useState("");return re.default.createElement(De,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature"},re.default.createElement("form",{onSubmit:async function(o){o.preventDefault(),d(""),a?._id===l._id&&r();const u=new t.DeleteFeatureChange({changedIds:[l._id],typeName:"DeleteFeatureChange",assembly:s,deletedFeature:i.getSnapshot(l),parentFeatureId:l.parent?._id});await e.submit(u),c("Feature deleted successfully","success"),n(),o.preventDefault()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.DialogContentText,null,"Are you sure you want to delete the selected feature?")),re.default.createElement(f.DialogActions,null,re.default.createElement(f.Button,{variant:"contained",type:"submit"},"Yes"),re.default.createElement(f.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),u?re.default.createElement(f.DialogContent,null,re.default.createElement(f.DialogContentText,{color:"error"},u)):null)}function ft({handleClose:e,session:a}){const[o,r]=h.useState(),[s,l]=h.useState(""),{collaborationServerDriver:c,getInternetAccount:u,inMemoryFileDriver:d}=a.apolloDataStore,m=[...c.getAssemblies(),...d.getAssemblies()];return re.default.createElement(De,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3"},re.default.createElement("form",{onSubmit:async function(r){if(r.preventDefault(),l(""),!o)return void l("Must select assembly to download");const{internetAccountConfigId:s}=n.getConf(o,["sequence","metadata"]);s?await async function(e){if(!o)return void l("Must select assembly to download");const t=u(o.configuration.name,e),n=new URL("export/getID",t.baseURL),a=new URLSearchParams({assembly:o.name});n.search=a.toString();const r=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:r}),i=await s(r,{method:"GET"});if(!i.ok){const e=await Ne(i,"Error when exporting ID");return void l(e)}const{exportID:c}=await i.json(),d=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c});d.search=f.toString();const m=d.toString();window.open(m,"_blank")}(s):function(e){if(!o)return void l("Must select assembly to download");const{assemblies:a}=e.apolloDataStore,r=a.get(o.name),s=r?.refSeqs;if(!s)return void l(`No refSeqs found for assembly "${o.name}"`);const c=[{directive:"gff-version",value:"3"}],u=n.getConf(o,["sequence","adapter","features"]);for(const e of u){const{end:t,refName:n,start:a}=e;c.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of s){const{features:n}=e;if(n)for(const[,e]of n)c.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const e of u){const{refName:t,seq:n}=e;c.push({id:t,description:"",sequence:n})}const d=ee.default.formatSync(c),f=new Blob([d],{type:"text/plain;charset=utf-8"});k.saveAs(f,`${o.displayName??o.name}.gff3`)}(a),e()}},re.default.createElement(f.DialogContent,{style:{display:"flex",flexDirection:"column"}},re.default.createElement(f.DialogContentText,null,"Select assembly"),re.default.createElement(f.Select,{labelId:"label",value:o?.name??"",onChange:function(e){const 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Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).actions((e=>({initialize:i.flow((function*(t){if("admin"===t){const t=i.getRoot(e);r.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Add Assembly",onClick:e=>{e.queueDialog((t=>[Me,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Delete Assembly",onClick:e=>{e.queueDialog((t=>[ut,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Import Features",onClick:e=>{e.queueDialog((t=>[mt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Ft,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Manage Users",onClick:e=>{e.queueDialog((t=>[ht,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Undo",onClick:e=>{const{apolloDataStore:t}=e,{notify:n}=e;t.changeManager.recentChanges.length>0?t.changeManager.revertLastChange():n("No changes to undo","info")}})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:n}=e,a=new URL("users/locations",n).href,o=e.getFetcher({locationType:"UriLocation",uri:a});yield o(a,{method:"GET"}),window.addEventListener("beforeunload",(()=>{e.postUserLocation([])})),document.addEventListener("visibilitychange",(()=>{if("hidden"===document.visibilityState&&e.postUserLocation([]),"visible"===document.visibilityState){const{session:t}=i.getRoot(e);t.broadcastLocations()}}))}))}))).actions((e=>({afterAttach(){e.setRole(),l.autorun((async t=>{if(Ot)return;const{session:n}=i.getRoot(e);n&&e.role&&(await 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this.regions=a,a}getFeatures(e,t){const{end:a,refName:o,start:r}=e,s=n.readConfObject(this.config,"assemblyId"),l={...e,assemblyName:s};return _.ObservableCreate((async e=>{if(!Wt){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)return void e.error("No Apollo data store found");const n=t.getBackendDriver(s),{seq:i}=await n.getSequence(l);return e.next(new ye.default({id:`${o} ${r}-${a}`,data:{refName:o,start:r,end:a,seq:i}})),void e.complete()}const n=await new Promise(((e,n)=>{const a=setTimeout((()=>{n("timeout")}),2e4),o=q.nanoid(),r=t=>{const{data:n}=t;Gt(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),e(n.sequence))};addEventListener("message",r,t),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:l,messageId:o})}));e.next(new ye.default({id:`${o} ${r}-${a}`,data:{refName:o,start:r,end:a,seq:n}})),e.complete()}))}freeResources(){}}var zt=n.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function Vt(e,t,n,a,o,r){const s=a/o;e.fillStyle="black",e.fillRect(t,n,s,r),s>2&&(e.clearRect(t+1,n+1,s-2,r-2),e.fillStyle="rgba(255,255,255,0.75)",e.fillRect(t+1,n+1,s-2,r-2))}var Jt=S.observer((function(e){const[a,o]=h.useState(),[s,c]=h.useState(),u=h.useRef(null),d=h.useRef(null),m=h.useRef(null),[g,p]=h.useState(!1),[y,b]=h.useState(!0),[S,w]=h.useState(),[v,C]=h.useState(!1),[E,x]=h.useState([]),{bpPerPx:A,displayModel:T,regions:k}=e,{session:N}=T,{collaborators:R}=N;h.useEffect((()=>l.autorun((()=>{x(l.toJS(R))}))),[]);const[D]=k,F=(D.end-D.start)/A,{apolloFeatureUnderMouse:M,apolloRowHeight:I,apolloRowUnderMouse:L,changeManager:q,codonLayout:P,featureLayout:U,features:B,featuresHeight:_,getAssemblyId:j,selectedFeature:O,setApolloFeatureUnderMouse:$,setApolloRowUnderMouse:G,setSelectedFeature:W,showIntronLines:H,showStartCodons:z,showStopCodons:V}=T,J=[...B.values()].map((e=>[...e.values()].map((e=>i.getSnapshot(e))))),X=h.useMemo((()=>{const{internetAccounts:e}=i.getRoot(N),{assemblyName:t}=D,{assemblyManager:a}=r.getSession(T),o=a.get(t);if(!o)throw new Error(`No assembly found with name 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0)},changeManager:q,sourceFeature:s,sourceAssemblyId:e}]))}},"Copy features and annotations"),re.default.createElement(f.MenuItem,{disabled:!g,key:3,value:3,onClick:()=>{if(!s)return;const e=j(D.assemblyName);N.queueDialog((t=>[dt,{session:N,handleClose:()=>{t(),c(void 0)},changeManager:q,sourceFeature:s,sourceAssemblyId:e,selectedFeature:O,setSelectedFeature:W}]))}},"Delete feature")),re.default.createElement("canvas",{ref:u,width:F,height:_,style:{position:"absolute",left:0,top:0}}),re.default.createElement("canvas",{ref:d,width:F,height:_,onMouseLeave:function(){$(),G()},onMouseUp:async function(){if(v){if(S){const e=j(D.assemblyName),{bp:n,edge:a,feature:o}=S;let r;if("end"===a){const a=o._id,s=o.max,l=Math.round(n);r=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[a],featureId:a,oldEnd:s,newEnd:l,assembly:e})}else{const a=o._id,s=o.min,l=Math.round(n);r=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[a],featureId:a,oldStart:s,newStart:l,assembly:e})}await q.submit(r)}}else M&&W(M);w(void 0),C(!1)},onContextMenu:function(e){e.preventDefault(),c(M),o([e.pageX,e.pageY])},style:{position:"absolute",left:0,top:0}}),re.default.createElement("canvas",{ref:m,width:F,height:6*I,style:{position:"absolute",left:0,top:0}}))})),Xt=n.ConfigurationSchema("ApolloSixFrameRenderer",{},{explicitlyTyped:!0});class Yt extends a.RendererType{async renderInClient(e,t){return this.render(t)}async freeResourcesInClient(e,t){return 0}}class Kt extends B.BaseAdapter{get baseURL(){return n.readConfObject(this.config,"baseURL").uri}get trackId(){return n.readConfObject(this.config,"trackId")}get assemblyNames(){return n.readConfObject(this.config,"assemblyNames")}mapBaseResult(e,t,n){return e.map((e=>{const a=t.getCanonicalRefName(e.refSeq);return new be.default({label:n,trackId:this.trackId,locString:`${a}:${e.min+1}..${e.max}`})}))}async searchIndex(e){const t=e.queryString,n=[],a=this.pluginManager?.rootModel?.session;if(!a)return n;const{apolloDataStore:o}=a,{assemblyManager:r}=a;for(const a of this.assemblyNames){const s=o.getBackendDriver(a),l=r.get(a);if(!s||!l)continue;const i=await s.searchFeatures(e.queryString,[a]);n.push(...this.mapBaseResult(i,l,t))}return n}freeResources(){}}var Zt=n.ConfigurationSchema("ApolloTextSearchAdapter",{assemblyNames:{type:"stringArray",defaultValue:[],description:"List of assemblies covered by text search adapter"},trackId:{type:"string",defaultValue:""},baseURL:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}}},{explicitlyTyped:!0,explicitIdentifier:"textSearchAdapterId"});const Qt=n.ConfigurationSchema("ApolloPlugin",{ontologies:i.types.array(tt),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"}});function en(e){if("LinearPileupDisplay"!==e.name)return e;const{stateModel:n}=e,a=n.views((e=>({getFirstRegion:()=>r.getContainingView(e).dynamicBlocks.contentBlocks[0],getAssembly(){const t=e.getFirstRegion(),n=r.getSession(e),{assemblyManager:a}=n,{assemblyName:o}=t,s=a.get(o);if(!s)throw new Error(`Could not find assembly named ${o}`);return s},getRefSeqId(t){const n=e.getFirstRegion(),{refName:a}=n,{refNameAliases:o}=t;if(!o)throw new Error(`Could not find aliases for ${t.name}`);const r=[...Object.entries(o)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t??""}))),s=r.find((e=>e.name===a))?._id;if(!s)throw new Error(`Could not find refSeqId named ${a}`);return s},createFeature(){const t=e.contextMenuFeature,n=e.getAssembly(),a=e.getRefSeqId(n),o=(t.get("CIGAR").toUpperCase().match(/\d+\D/g)??[]).map((e=>[(/\D/.exec(e)??[])[0],Number.parseInt(e,10)]));let r=0;const s=t.get("start");let l;const i=[];for(const[e,t]of o)"M"===e||"="===e?void 0===l&&(l=r+s):"N"===e&&void 0!==l&&(i.push({start:l,end:r+l}),l=void 0),"I"!==e&&(r+=t);void 0!==l&&i.push({start:l,end:r+s});const c={_id:oe.default().toHexString(),refSeq:a,min:t.get("start"),max:t.get("end"),type:"mRNA",strand:t.get("strand")};if(0===i.length)return c;c.children={};const[u]=i,d={_id:oe.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"CDS",strand:t.get("strand")};if(c.children[d._id]=d,1===i.length){const e={_id:oe.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"exon",strand:t.get("strand")};return c.children[e._id]=e,c}for(const e of i){d.min=Math.min(d.min,e.start),d.max=Math.max(d.max,e.end);const{end:n,start:o}=e,r={_id:oe.default().toHexString(),refSeq:a,min:o,max:n,type:"exon",strand:t.get("strand")};c.children[r._id]=r}return c},async onPileupFeatureContext(){const n=e.createFeature(),a=e.getAssembly(),o=new t.AddFeatureChange({changedIds:[n._id],typeName:"AddFeatureChange",assembly:a.name,addedFeature:n}),s=r.getSession(e);await s.apolloDataStore.changeManager.submit(o),s.notify("Annotation added 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Ontology"})]]),an=["ID","Name","Alias","Target","Gap","Derives_from","Note","Dbxref","Ontology","Is_Circular"],on=w.makeStyles()((e=>({newAttributePaper:{padding:e.spacing(2)},attributeName:{background:e.palette.secondary.main,color:e.palette.secondary.contrastText,padding:e.spacing(1)}})));function rn(e){const{onChange:t,value:n}=e;return re.default.createElement(tn,{value:n,onChangeCommitted:e=>{t(e.split(","))},variant:"outlined",fullWidth:!0,helperText:"Separate multiple values for the attribute with commas"})}const sn=S.observer((function({assembly:e,editable:n,feature:a,session:o}){const[r,s]=h.useState(""),[l,c]=h.useState(!1),{classes:u}=on(),[d,m]=h.useState(""),g=Object.fromEntries([...a.attributes.entries()].map((([e,t])=>{if(e.startsWith("gff_")){const n=e.slice(4);return[n.charAt(0).toUpperCase()+n.slice(1),i.getSnapshot(t)]}return"_id"===e?["ID",i.getSnapshot(t)]:[e,i.getSnapshot(t)]}))),{notify:p}=o,{changeManager:y}=o.apolloDataStore;async function b(n,o){s("");const r={};if(g){const e=Object.entries({...g,[n]:o});for(const[t,n]of e)if(n&&"parent"!==t.toLowerCase())if([...nn.keys()].includes(t))r[t]=n;else switch(t){case"ID":r._id=n;break;case"Name":r.gff_name=n;break;case"Alias":r.gff_alias=n;break;case"Target":r.gff_target=n;break;case"Gap":r.gff_gap=n;break;case"Derives_from":r.gff_derives_from=n;break;case"Note":r.gff_note=n;break;case"Dbxref":r.gff_dbxref=n;break;case"Ontology_term":r.gff_ontology_term=n;break;case"Is_circular":r.gff_is_circular=n;break;default:r[t.toLowerCase()]=n}}const l=new t.FeatureAttributeChange({changedIds:[a._id],typeName:"FeatureAttributeChange",assembly:e,featureId:a._id,attributes:r});await y.submit(l),p("Feature attributes modified successfully","success")}return re.default.createElement(re.default.Fragment,null,re.default.createElement(f.Typography,{variant:"h5"},"Attributes"),re.default.createElement(f.Grid,{container:!0,direction:"column",spacing:1},Object.entries(g).map((([e,t])=>{if(""===e)return null;const a=nn.get(e)??rn;return re.default.createElement(f.Grid,{container:!0,item:!0,spacing:3,alignItems:"center",key:e},re.default.createElement(f.Grid,{item:!0,xs:"auto"},re.default.createElement(f.Paper,{variant:"outlined",className:u.attributeName},re.default.createElement(f.Typography,null,e))),re.default.createElement(f.Grid,{item:!0,flexGrow:1},re.default.createElement(a,{session:o,value:t,onChange:t=>b(e,t)})),re.default.createElement(f.Grid,{item:!0,xs:1},re.default.createElement(f.IconButton,{"aria-label":"delete",size:"medium",disabled:!n,onClick:()=>b(e)},re.default.createElement(fe.default,{fontSize:"medium",key:e}))))})),re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.Button,{color:"primary",variant:"contained",disabled:l||!n,onClick:()=>{c(!0)}},"Add new")),l?re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.Paper,{elevation:8,className:u.newAttributePaper},re.default.createElement(f.Grid,{container:!0,direction:"column"},re.default.createElement(f.Grid,{item:!0},re.default.createElement(f.FormControl,null,re.default.createElement(f.FormLabel,{id:"attribute-radio-button-group"},"Select attribute type"),re.default.createElement(f.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:"custom",name:"radio-buttons-group",onChange:function(e,t){"custom"===t?m(""):nn.has(t)?m(t):s("Unknown attribute 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re.default.createElement("div",{onMouseDown:e=>{e.stopPropagation(),globalThis.addEventListener("mousemove",n),globalThis.addEventListener("mouseup",a),globalThis.addEventListener("mouseleave",a)},onClick:e=>{e.stopPropagation(),e.preventDefault()},className:t.resizeHandle})},Na=S.observer((function({onClick:e,onResize:t,open:n,title:a}){const{classes:o}=Ta();return re.default.createElement("div",{className:o.accordionRoot},n&&t?re.default.createElement(ka,{onResize:t}):null,re.default.createElement("div",{className:o.accordionControl,onClick:e},re.default.createElement(n?ve.default:Ce.default,{className:o.expandIcon}),a?re.default.createElement(f.Typography,{className:o.title,variant:"caption",component:"span"},a):null))})),Ra=S.observer((function({model:e,...t}){const n=r.getSession(e),{ontologyManager:a}=n.apolloDataStore,{featureTypeOntology:o}=a,s=o?.dataStore,{classes:l}=Ta(),{detailsHeight:i,graphical:c,height:u,isShown:d,selectedFeature:m,table:g,tabularEditor:p,toggleShown:y}=e,b=h.useRef(null);h.useEffect((()=>{!function(e,t){const{apolloRowHeight:n,selectedFeature:a}=e;if(t.current&&a){const o=e.getFeatureLayoutPosition(a);o&&t.current.scroll({top:(o.layoutRow+o.featureRow)*n,behavior:"smooth"})}}(e,b)}),[e,m]);const S=t=>{e.setDetailsHeight(i-t)};if(!s)return re.default.createElement("div",{className:l.alertContainer},re.default.createElement(f.Alert,{severity:"error"},"Could not load feature type ontology."));if(c&&g){const n=p.isShown?i:0,a=d?u-i-24:0;return 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n||(n=r.getSession(e).addWidget("JobsListWidget","JobsList")),n}}))).actions((e=>({update(t,n,a){e.jobStatusWidget.updateJobStatusMessage(t,n),a&&e.jobStatusWidget.updateJobProgressPct(t,a)},abortJob(t,n){const a=r.getSession(e);if(r.isSessionModelWithWidgets(a)){a.showWidget(e.jobStatusWidget),e.jobStatusWidget.updateJobStatusMessage(t,n??"Aborted unexpectedly");const o=e.jobStatusWidget.jobs.findIndex((e=>e.name===t));e.jobStatusWidget.addAbortedJob({...e.jobStatusWidget.jobs[o]}),e.jobStatusWidget.removeJob(t),a.notify("Job aborted","info")}},runJob(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.removeJob(t.name),e.jobStatusWidget.addFinishedJob({name:t.name,statusMessage:"All operations successful",progressPct:100,cancelCallback:t.cancelCallback}))}})));class Fa{clientStore;constructor(e){this.clientStore=e}}class Ma{dataStore;constructor(e){this.dataStore=e}recentChanges=[];async submit(n,a={}){const{addToRecents:o=!0,submitToBackend:s=!0,updateJobsManager:l=!1}=a,i=r.getSession(this.dataStore),c=new AbortController,{jobsManager:u}=r.getSession(this.dataStore),d={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort()}};l&&u.runJob(d);const f=await t.validationRegistry.frontendPreValidate(n);if(!f.ok){const e=`Pre-validation failed: "${f.resultsMessages}"`;return l&&u.abortJob(d.name,e),void i.notify(e,"error")}try{await n.execute(this.dataStore)}catch(e){return l&&u.abortJob(d.name,String(e)),console.error(e),void i.notify(String(e),"error")}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.revert(n),s){l&&u.update(d.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:o}=this.dataStore,r=e.isAssemblySpecificChange(n)?o(n.assembly):t;let s;try{s=await r.submitChange(n,a)}catch(e){return l&&u.abortJob(d.name,String(e)),console.error(e),i.notify(String(e),"error"),void await this.revert(n,!1)}if(!s.ok){const e=`Post-validation failed: "${f.resultsMessages}"`;return l&&u.abortJob(d.name,e),i.notify(e,"error"),void await this.revert(n,!1)}n.notification&&i.notify(n.notification,"success")}o&&this.recentChanges.push(n),l&&u.done(d)}async revert(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async revertLastChange(){const e=this.recentChanges.pop();if(e)return this.revert(e);r.getSession(this.dataStore).notify("No changes to undo!","warning")}}class Ia extends Fa{inFlight=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:a}=n,o=new URL("features/searchFeatures",a),r=new URLSearchParams({assemblies:t.join(","),term:e});o.search=r.toString();const s=o.toString(),l=await this.fetch(n,s);if(!l.ok){const e=await Ne(l,"searchFeatures failed");throw new Error(e)}return l.json()}async getFeatures(e){const{assemblyName:t,end:a,refName:o,start:s}=e,{assemblyManager:l}=r.getSession(this.clientStore),i=l.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=n.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(s),end:String(a)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await Ne(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),s=`${t}-${n}`,l=new Ma(this.clientStore);o.hasListeners(s)||o.on(s,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===s){const n=e.Change.fromJSON(t.changeInfo);await l.submit(n,{submitToBackend:!1})}}))}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,a=this.inFlight.get(t),{assemblyName:o,end:s,refName:l,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=n.getConf(u,["sequence","metadata"]),f=d[l];if(!f)throw new Error(`Could not find refSeq "${l}"`);if(a)return{seq:await a,refSeq:f};let m=this.clientStore.assemblies.get(o);m||(m=this.clientStore.addAssembly(o));let g=m.refSeqs.get(f);g||(g=m.addRefSeq(f,l));const p=g.getSequence(i,s);if(p.length===s-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(s)});b.search=S.toString();const w=b.toString(),v=this.getSeqFromServer(h,w,g,i,s);this.inFlight.set(t,v);const C=await v;return this.checkSocket(o,l,h),this.inFlight.delete(t),{seq:C,refSeq:f}}async getSeqFromServer(e,t,n,a,o){const r=await this.fetch(e,t);if(!r.ok){let e;try{e=await r.text()}catch{e=""}throw new Error(`getSequence failed: ${r.status} (${r.statusText})${e?` (${e})`:""}`)}const s=await r.text();return n.addSequence({sequence:s,start:a,stop:o}),s}async getRefNameAliases(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),s=new URLSearchParams({assembly:e});o.search=s.toString();const l=o.toString(),i=await this.fetch(n,l);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),s=new URLSearchParams({assembly:e});o.search=s.toString();const l=o.toString(),i=await this.fetch(n,l);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRegions failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(e){const{assemblyManager:t}=r.getSession(this.clientStore);return t.assemblies.filter((t=>{const a=n.getConf(t,["sequence","metadata"]);return!(!(a&&a.apollo&&a.internetAccountConfigId)||e&&a.internetAccountConfigId!==e)}))}async submitChange(e,n={}){const{internetAccountId:a}=n,o=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,a),{baseURL:r}=o,s=new URL("changes",r).href,l=await this.fetch(o,s,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!l.ok){const e=await Ne(l,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return l.ok||(i.ok=!1),i}}class La extends Fa{async getFeatures(){return[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=this.clientStore.assemblies.get(t);if(!r)return{seq:"",refSeq:a};const s=r.refSeqs.get(a);return s?{seq:s.getSequence(o,n),refSeq:a}:{seq:"",refSeq:a}}async getRefNameAliases(e){const t=this.clientStore.assemblies.get(e),n=[];if(!t)return n;for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getRegions(e){const t=this.clientStore.assemblies.get(e);if(!t)return[];const n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=n.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){const{clientStore:a}=this,{assemblies:o}=a;a.clearCheckResults();for(const[,e]of o)if("InMemoryFileDriver"===e.backendDriverType){const t=await ke(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class qa extends Fa{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),a=t.get(e);if(!a)throw new Error(`Assembly ${e} not found`);const{file:o}=n.getConf(a,["sequence","metadata"]),s=require("node:fs");return Te(e,await s.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=(await this.getAssembly(t)).refSeqs.get(a);if(!r)throw new Error(`refSeq ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=n.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(a){if(!e.isAssemblySpecificChange(a))throw new Error(`Cannot use this type of change with local file: "${a.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),s=o.get(a.assembly);if(!s)throw new Error(`Could not find assembly with name "${a.assembly}"`);const{file:l}=n.getConf(s,["sequence","metadata"]),c=this.clientStore.assemblies.get(a.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${a.assembly}"`);const u=new Set(...c.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await ke(c);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=ee.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(l,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function Pa(e,a){const o=new AbortController,{signal:s}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",$.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map($.ApolloAssembly),checkResults:i.types.map($.CheckResult),ontologyManager:i.types.optional(Qe,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):i.getParentOfType(n,$.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Ma(e),collaborationServerDriver:new Ia(e),inMemoryFileDriver:new La(e),desktopFileDriver:r.isElectron?new qa(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,l.autorun((()=>{const{ontologyManager:t,pluginConfiguration:a}=e,o=a.ontologies;for(const e of o||[]){const[a,o,r,s]=[n.readConfObject(e,"name"),n.readConfObject(e,"version"),n.readConfObject(e,"source"),n.readConfObject(e,"textIndexFields")];t.findOntology(a)||t.addOntology(a,o,r,{textIndexing:{indexFields:s}})}})))}}))).views((e=>({getBackendDriver(t){if(!t)return e.collaborationServerDriver;const a=r.getSession(e),{assemblyManager:o}=a,s=o.get(t);if(!s)return e.collaborationServerDriver;const{file:l,internetAccountConfigId:i}=n.getConf(s,["sequence","metadata"]);return r.isElectron&&l?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,a){if(!(t??a))throw new Error("Must provide either assemblyName or internetAccountId");let o=a;if(t&&!o){const{assemblyManager:a}=r.getSession(e),s=a.get(t);if(!s)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=n.getConf(s,["sequence","metadata"]))}const{internetAccounts:s}=e,l=s.find((e=>e.internetAccountId===o));if(!l)throw new Error(`No InternetAccount found with config id ${a}`);return l}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:s}=n;let l=e.assemblies.get(r);l||(l=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=l.refSeqs.get(i.refSeq);c||(c=l.refSeqs.put({_id:i.refSeq,name:s,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:s,refName:l,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:l,sequence:[]})),u.addSequence({start:i,stop:s,sequence:o})}}))})))}(c),d=a.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(Da,{})}).extend((()=>{const e=l.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,a){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${n.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...a?{baseURL:{uri:a,locationType:"UriLocation"}}:{}}},displays:[{type:"LinearApolloDisplay",displayId:`${o}-LinearApolloDisplay`},{type:"SixFrameFeatureDisplay",displayId:`${o}-SixFrameFeatureDisplay`}]})},broadcastLocations(){const{internetAccounts:t}=i.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:s}=t,l=e.apolloDataStore.assemblies.get(a);l&&"CollaborationServerDriver"===l.backendDriverType&&n.push({assemblyName:a,refName:r,start:s,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).actions((e=>({afterCreate:i.flow((function*(){const t=i.getSnapshot(e),{id:n,name:a}=t;i.applySnapshot(e,{name:a,id:n});const{internetAccounts:o,jbrowse:r}=i.getRoot(e);l.autorun((()=>{const t=[];for(const n of e.views){if("LinearGenomeView"!==n.type)return;const a=n;if(a.initialized){const{dynamicBlocks:n}=a;n.forEach((n=>{if(void 0!==n.regionNumber){const{assemblyName:a,end:o,refName:r,start:s}=n,l=e.apolloDataStore.assemblies.get(a);l&&"CollaborationServerDriver"===l.backendDriverType&&t.push({assemblyName:a,refName:r,start:s,end:o})}}))}}if(0===t.length){for(const e of o)"baseURL"in e&&e.postUserLocation([]);return}const n=[];for(const e of o)if("baseURL"in e){for(const e of t)n.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(n)}}),{name:"ApolloSession"});for(const n of o){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:a}=n,o=new URL("jbrowse/config.json",a).href,l=n.getFetcher({locationType:"UriLocation",uri:o});let c,u;try{c=yield l(o,{signal:s})}catch(e){console.error(e);continue}if(c.ok){try{u=yield c.json()}catch(e){console.error(e);continue}i.applySnapshot(r,u),i.applySnapshot(e,t)}else{const e=yield Ne(c,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const a=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return a?.(o);const r=n.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...a?.(o)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),s=i.getSnapshot(a);let l;l=t.filterJBrowseConfig(s),0===Object.keys(l).length&&(l=void 0);const c={...i.getSnapshot(o),trackId:r.slice(0,r.length-13)};for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:l,newJBrowseConfig:{...l,tracks:l?.tracks&&[...l.tracks,c]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(c)},icon:xe.default}]:[...a?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),s=i.getSnapshot(a);let l;l=t.filterJBrowseConfig(s),0===Object.keys(l).length&&(l=void 0);const c=l?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:l,newJBrowseConfig:{...l,tracks:c}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:xe.default}]}}}));return i.types.snapshotProcessor(d,{postProcessor(e,t){e.apolloSelectedFeature=void 0;const n=Object.fromEntries(Object.entries(e.apolloDataStore.assemblies).filter((([,e])=>"InMemoryFileDriver"===e.backendDriverType)));if(e.apolloDataStore={typeName:"Client",assemblies:n,checkResults:{}},!t)return e;const{apolloDataStore:a}=t,{checkResults:o}=a;for(const[,t]of o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=i.getSnapshot(t))}return e}})}const Ua={0:2,1:1,2:0},Ba={3:0,4:1,5:2};function _a(e,t){const a=e.getPlugin("LinearGenomeViewPlugin"),{BaseLinearDisplay:o}=a.exports;return o.named("SixFrameFeatureDisplay").props({type:i.types.literal("SixFrameFeatureDisplay"),configuration:n.ConfigurationReference(t),apolloRowHeight:20,detailsMinHeight:200,showStartCodons:!1,showStopCodons:!0,showIntronLines:!0}).volatile((()=>({apolloFeatureUnderMouse:void 0,apolloRowUnderMouse:void 0}))).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...G.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get regions(){let t;try{({blockDefinitions:t}=e)}catch{return[]}return t.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))},regionCannotBeRendered(){const t=r.getContainingView(e);if(t&&t.bpPerPx>=200)return"Zoom in to see annotations"},get session(){return r.getSession(e)}}))).actions((e=>{let t=[];return{afterAttach(){i.addDisposer(e,l.autorun((()=>{const n=r.getSession(e);if(r.getContainingView(e).initialized){if(e.regionCannotBeRendered())return;const a=[],o=[];for(const n of e.blockDefinitions.contentBlocks)a.push(n.key),t.includes(n.key)||o.push(n);n.apolloDataStore.loadFeatures(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),n.apolloDataStore.loadRefSeq(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),t=a}}),{name:"SixFrameFeatureDisplay"}))}}})).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get changeManager(){return r.getSession(e).apolloDataStore.changeManager},get sequence(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName),r=o?.getSequence(e.start,e.end);a.set(e.start,r??"")}return a},get features(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName);let r=a.get(e.refName);r||(r=new Map,a.set(e.refName,r));for(const[t,n]of o?.features.entries()??new Map)e.start<n.end&&e.end>n.start&&r.set(t,n)}return a},get featuresMinMax(){const e={};for(const[t,n]of this.features||[]){let a,o;for(const[,e]of n)void 0===a&&({min:a}=e),void 0===o&&({max:o}=e),e.min<a&&({min:a}=e),e.max>o&&({max:o}=e);void 0!==a&&void 0!==o&&(e[t]=[a,o])}return e},get codonLayout(){const e=new Map;let t="",n=0;for(const[e,a]of this.sequence||[])a&&(t||(n=e),t+=a);for(let a=0;a<6;a++){const o=[],s=[],l=a in Ba;let i,c,u;l?(i=(t.length+n)%3,c=(Ba[a]+i+3)%3,u=r.reverse(t).slice(c)):(i=3-n%3,c=(Ua[a]+i+3)%3,u=t.slice(c));for(let e=0;e<u.length;e+=3){const t=u.slice(e,e+3),a=l?r.reverse(r.revcom(t)):t,i=l?n+u.length-(3+e):n+e+c;r.defaultStarts.includes(a.toUpperCase())?o.push(i):r.defaultStops.includes(a.toUpperCase())&&s.push(i)}e.set(a,{starts:o,stops:s})}return e},get featureLayout(){const e=new Map;for(const[t,n]of this.features||[]){if(!n)continue;const a=this.featuresMinMax[t];if(!a)continue;const[o,r]=a,s=[],l=6;for(let t=0;t<l;t++){const t=s.length;s[t]=Array.from({length:r-o}),e.set(t,[])}for(const t of[...n.values()].sort(((e,t)=>{const{max:n,min:a}=e,{max:o,min:r}=t;return a-r||n-o})))for(const[,n]of t.children??new Map)if("mRNA"===n.type)for(const[,a]of n.children||new Map){let o;if("CDS"===a.type){let r;a.discontinuousLocations.length>0?({discontinuousLocations:r}=a):r=[a];for(const a of r){const r=a.start+3,s=a.end-3;for(const[l,{stops:i}]of this.codonLayout)if((l<3&&1===t.strand||l>=3&&-1===t.strand)&&0===i.filter((e=>e>=r&&e<=s)).length){o=l;const t=e.get(o);t?.push([n.featureId,a]);break}}}}}return e},getAssemblyId(t){const{assemblyManager:n}=r.getSession(e),a=n.get(t);if(!a)throw new Error(`Could not find assembly named ${t}`);return a.name},get selectedFeature(){return r.getSession(e).apolloSelectedFeature},get setSelectedFeature(){return r.getSession(e).apolloSetSelectedFeature}}))).actions((e=>({setSelectedFeature(t){r.getSession(e).apolloSetSelectedFeature(t)},setApolloFeatureUnderMouse(t){e.apolloFeatureUnderMouse=t},setApolloRowUnderMouse(t){e.apolloRowUnderMouse=t},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleShowIntronLines(){e.showIntronLines=!e.showIntronLines}}))).views((e=>({get highestRow(){return 0===e.featureLayout.size?0:Math.max(...e.featureLayout.keys())},get featuresHeight(){return(this.highestRow+1)*e.apolloRowHeight},get detailsHeight(){return Math.max(e.detailsMinHeight,e.height-this.featuresHeight)},trackMenuItems:()=>[{label:"Show start codons",type:"checkbox",checked:e.showStartCodons,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:e.showStopCodons,onClick:()=>{e.toggleShowStopCodons()}},{label:"Show intron lines",type:"checkbox",checked:e.showIntronLines,onClick:()=>{e.toggleShowIntronLines()}}]})))}var ja=n.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});const Oa="undefined"==typeof sessionStorage;class $a extends B.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=n.readConfObject(this.config,"assemblyId");if(!Oa){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);return await n.getRefNameAliases(e)}const t=await new Promise(((t,n)=>{const a=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=q.nanoid(),r=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in e})(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),t(n.refNameAliases))};addEventListener("message",r),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:o})}));return this.refNameAliases=t,t}freeResources(){}}const Ga="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Wa=new t.CDSCheck;e.checkRegistry.registerCheck(Wa.name,Wa),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends Z.default{name="ApolloPlugin";version="0.2.2";configurationSchema=Qt;install(e){!function(e){e.addAdapterType((()=>new he.default({name:"ApolloSequenceAdapter",configSchema:zt,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Ht})))}(e),function(e){e.addAdapterType((()=>new he.default({name:"ApolloRefNameAliasAdapter",configSchema:ja,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:$a})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:Zt,AdapterClass:Kt,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new a.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:gn,ReactComponent:mn})})),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloTranscriptDetails",{});return new a.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:pn,ReactComponent:vn})})),e.addTrackType((()=>{const t=n.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a.TrackType({name:"ApolloTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new a.InternetAccountType({name:"ApolloInternetAccount",configSchema:Ae,stateModel:$t(Ae)}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloDisplay",configSchema:Cn,stateModel:Ca(0,Cn),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Ra}))),e.addDisplayType((()=>{const t=function(e){const t=e.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=t.exports;return n.ConfigurationSchema("SixFrameFeatureDisplay",{renderer:Xt,height:{type:"number",defaultValue:120}},{baseConfiguration:a,explicitlyTyped:!0})}(e),o=function(e){const t=e.getPlugin("LinearGenomeViewPlugin");if(!t)throw new Error("LinearGenomeView plugin not found");const{BaseLinearDisplayComponent:n}=t.exports;return S.observer((function({model:e,...t}){const{classes:a}=Ta(),{height:o,selectedFeature:r}=e;let{detailsHeight:s}=e;return r||(s=0),re.default.createElement("div",{style:{height:e.height}},re.default.createElement("div",{className:a.shading,style:{height:o-s}},re.default.createElement(n,{model:e,...t})),re.default.createElement("div",{className:"testTrackLines"},re.default.createElement(Aa,{model:e})))}))}(e);return new a.DisplayType({name:"SixFrameFeatureDisplay",configSchema:t,stateModel:_a(e,t),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((()=>new Yt({name:"ApolloSixFrameRenderer",ReactComponent:Jt,configSchema:Xt,pluginManager:e}))),e.addToExtensionPoint("Core-extendSession",Pa.bind(this,e)),e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearGenomeView"===e.name){const{stateModel:t}=e,n=t.views((e=>{const t=e.rubberBandMenuItems;return{rubberBandMenuItems:()=>[...t(),{label:"Add new feature",icon:Q.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[lt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",en),Ga||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t&&t.on?(t.on("apollo",(async n=>{if("object"!=typeof(a=n)||null===a||!("apollo"in a)||!0!==a.apollo)return;var a;const{apollo:o,messageId:r,method:s}=n;switch(s){case"getSequence":{const{region:a}=n,{assemblyName:s}=a,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const i=l.getBackendDriver(s),{seq:c}=await i.getSequence(a);t.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=n,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a),i=await l.getRegions(a);t.workers[0].postMessage({apollo:o,messageId:r,regions:i});break}case"getRefNameAliases":{const{assembly:a}=n,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a),i=await l.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[pt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Nt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[Tt,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[Mt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Log out",onClick:e=>{e.queueDialog((t=>[gt,{session:e,handleClose:()=>{t()}}]))}}))}};
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