@apollo-annotation/jbrowse-plugin-apollo 0.1.0 → 0.1.1

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

@@ -1,2 +1,2 @@
-"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@jbrowse/core/configuration"),t=require("@jbrowse/core/pluggableElementTypes"),n=require("@jbrowse/core/Plugin"),a=require("@jbrowse/core/util"),o=require("@mui/icons-material/Add"),r=require("apollo-common"),s=require("apollo-shared"),i=require("mobx"),l=require("mobx-state-tree"),c=require("socket.io-client"),u=require("@gmod/gff"),d=require("nanoid"),f=require("@mui/icons-material/Link"),g=require("@mui/material"),m=require("@mui/material/InputAdornment"),h=require("@mui/material/LinearProgress"),p=require("bson-objectid"),y=require("react"),b=require("@jbrowse/core/ui"),w=require("@mui/icons-material/Close"),S=require("mobx-react"),v=require("tss-react/mui"),C=require("@jbrowse/core/util/types/mst"),E=require("jsonpath"),x=require("@jbrowse/core/util/io"),F=require("fast-deep-equal/es6"),A=require("idb/with-async-ittr"),D=require("file-saver"),k=require("@mui/material/Checkbox"),M=require("@mui/material/FormControlLabel"),R=require("@mui/icons-material/Delete"),L=require("@mui/x-data-grid"),N=require("@mui/material/utils"),T=require("autosuggest-highlight/match"),I=require("autosuggest-highlight/parse"),P=require("@mui/icons-material/AccountCircle"),q=require("@jbrowse/core/pluggableElementTypes/AdapterType"),_=require("@jbrowse/core/data_adapters/BaseAdapter"),U=require("@jbrowse/core/util/rxjs"),O=require("@jbrowse/core/util/simpleFeature"),B=require("@jbrowse/core/TextSearch/BaseResults"),j=require("@mui/icons-material/Clear"),$=require("@mui/icons-material/UnfoldLess"),G=require("@jbrowse/core/util/tracks"),H=require("@mui/icons-material/ExpandLess"),W=require("@mui/icons-material/ExpandMore"),z=require("@mui/material/styles"),V=require("@mui/icons-material/Error"),J=require("apollo-mst");function X(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}function Y(e){if(e&&e.__esModule)return e;var t=Object.create(null);return e&&Object.keys(e).forEach((function(n){if("default"!==n){var a=Object.getOwnPropertyDescriptor(e,n);Object.defineProperty(t,n,a.get?a:{enumerable:!0,get:function(){return e[n]}})}})),t.default=e,t}var Z=X(n),K=X(o),Q=X(u),ee=X(f),te=X(m),ne=X(h),ae=X(p),oe=X(y),re=Y(y),se=X(w),ie=X(E),le=X(F),ce=X(k),ue=X(M),de=X(R),fe=X(T),ge=X(I),me=X(P),he=X(q),pe=X(O),ye=X(B),be=X(j),we=X($),Se=X(H),ve=X(W),Ce=X(V);const Ee=e.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:t.BaseInternetAccountConfig,explicitlyTyped:!0});async function xe(e,t,n){const 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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 Te(e,t){for(const[n,a]of t.entries())if(e.startsWith(a))return e.replace(a,n);return e}const Ie="$PREFIXED_ID";function Pe(e,t,n){return t===Ie?[Te(e.id,n)]:ie.default.query(e,t)}function qe(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!Ne.has(e)))}function*_e(e){for(const t of e)yield*qe(t)}function*Ue(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=ie.default.query(t,"$..*");yield*Ue(e)}}function*Oe(e,t,n){for(const a of t){const t=Pe(e,a,n);if(t.length>0)for(const e of _e(Ue(t)))yield[a,e]}}async function Be(e,t,n){const o=await this.db,r=t??o.transaction(["nodes"]);a.checkAbortSignal(n);const s=[...qe(e)],i=[],l=new Map;i.push(...s.map((async(e,t)=>{a.checkAbortSignal(n);const o=r.objectStore("nodes").index("full-text-words");for await(const r of o.iterate(IDBKeyRange.bound(e,`${e}￿`,!1,!1))){a.checkAbortSignal(n);const e=r.value,o=l.get(e.id)??[e,new Set];o[1].add(t),l.set(e.id,o)}}))),await Promise.all(i),a.checkAbortSignal(n);const c=[];for(const[,[e,t]]of l)a.checkAbortSignal(n),c.push(...je(this.textIndexFields,e,t,s,this.prefixes));return c.sort(((e,t)=>t.score-e.score)),c.slice(0,this.options.maxSearchResults??this.DEFAULT_MAX_SEARCH_RESULTS)}function je(e,t,n,a,o){const r=[...n].sort().map((e=>a[e])),s=r.map((e=>{const t=e.replaceAll(/[$()*+./?[\\\]^{|}-]/g,"\\$&");return new RegExp(`\\b${t}`,"gi")}));let i=[],l=0;for(const[n,r]of e.entries()){const c=new Set,u=e.length-n-1,d=[...Ue(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,i=a[t];void 0!==r&&(n+=.01*i.length,n+=i.length/e.length*100*.05,o.push({wordIndex:t,position:r}))}n+=100*c.size,l<n&&(l=n),o.sort(((e,t)=>e.position-t.position)),o.length>0&&i.push({term:t,field:r,str:e,score:n,wordMatches:o})}}i=i.filter((e=>e.score===l));for(const e of i){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 i}function $e(e){return"string"==typeof e.id}function Ge(e){return"string"==typeof e.sub&&"string"==typeof e.pred&&"string"==typeof e.obj}function He(e){return Boolean(e.meta?.deprecated)}async function We(e){return A.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 ze(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function Ve(e){const t=Date.now(),n=JSON.parse(await x.openLocation(this.sourceLocation).readFile("utf8")),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=Je.call(this).map((e=>e.jsonPath));for(const e of 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nt(e){return"PROPERTY"===e.type}function at({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:o,ontologyName:r,ontologyVersion:s,renderInput:i,session:l,style:c,value:u}){const[d,f]=y.useState(!1),[m,h]=y.useState(),[p,b]=y.useState(""),[w,S]=y.useState(),v=l.apolloDataStore.ontologyManager,C=v.findOntology(r,s)?.dataStore,E=C&&d&&!m,x=C&&!w,F=y.useCallback((e=>(n||!He(e))&&(!t||t(e))),[t,n]);y.useEffect((()=>{d||h(void 0)}),[d]),y.useEffect((()=>{const e=new AbortController,{signal:t}=e;return x&&(b(""),async function(e,t,n,a){if(!t)return;const o=(await e.getTermsWithLabelOrSynonym(t,{includeSubclasses:!1})).find(n??(()=>!0));if(!o)throw new Error(`not a valid ${e.ontologyName} term`);return o}(C,u,F).then((e=>{t.aborted||S(e)}),(e=>{t.aborted||a.isAbortException(e)||b(String(e))}))),()=>{e.abort()}}),[l,u,F,C,x]),y.useEffect((()=>{const t=new AbortController,{signal:n}=t;return E&&async function(e,t,n,a){let o;if(t){const n=await t(e,a);n&&(o=n)}return o||(o=await 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rt({changeManager:e,handleClose:t,session:n,sourceAssemblyId:a,sourceFeature:o}){const{notify:r}=n,[i,l]=y.useState(String(o.end)),[c,u]=y.useState(String(o.start+1)),[d,f]=y.useState(""),[m,h]=y.useState(""),[p,b]=y.useState(),[w,S]=y.useState(!1),[v,C]=y.useState(""),[E,x]=y.useState(""),F=Number(i)<=Number(c);return oe.default.createElement(Me,{open:!0,title:"Add new child feature",handleClose:t,maxWidth:!1,"data-testid":"add-feature-dialog"},oe.default.createElement("form",{onSubmit:async function(n){if(n.preventDefault(),C(""),w&&""===m)return void C("The phase is REQUIRED for all CDS features.");const l=new s.AddFeatureChange({changedIds:[o._id],typeName:"AddFeatureChange",assembly:a,addedFeature:{_id:(new ae.default).toHexString(),gffId:"",refSeq:o.refSeq,start:Number(c)-1,end:Number(i),type:d,phase:p},parentFeatureId:o._id});await(e.submit?.(l)),r("Feature added 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it({changeManager:t,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{assemblyManager:i,notify:c}=a,u=i.assemblyList,[d,f]=y.useState(u.find((e=>e.name!==o))?.name),[m,h]=y.useState([]),[p,b]=y.useState(""),[w,S]=y.useState(r.start),[v,C]=y.useState("");function E(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=E(a,t);ae.default.isValid(e.gffId.toString())&&(e.gffId=e._id),e.refSeq=p,e.start=e.start+t,e.end=e.end+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 y.useEffect((()=>{b(""),async function(){if(!d)return void C("No assemblies to copy to");const e=await i.waitForAssembly(d);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const 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0===o&&r(S[0])}),[S,o]),oe.default.createElement(Me,{open:!0,title:"Delete Assembly",handleClose:t,maxWidth:!1,"data-testid":"delete-assembly"},oe.default.createElement("form",{onSubmit:async function(n){if(n.preventDefault(),m(!0),c(""),!o)return void c("Must select assembly!");const a=new s.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:o.name});await(e.submit?.(a,{internetAccountId:p.internetAccountId})),t(),n.preventDefault()}},oe.default.createElement(g.DialogContent,{style:{display:"flex",flexDirection:"column"}},h.length>1?oe.default.createElement(oe.default.Fragment,null,oe.default.createElement(g.DialogContentText,null,"Select account"),oe.default.createElement(g.Select,{value:p.internetAccountId,onChange:function(e){m(!1);const t=h.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID 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successfully","success"),t(),a.preventDefault()}},oe.default.createElement(g.DialogContent,{style:{display:"flex",flexDirection:"column"}},oe.default.createElement(g.DialogContentText,null,"Are you sure you want to delete the selected feature?")),oe.default.createElement(g.DialogActions,null,oe.default.createElement(g.Button,{variant:"contained",type:"submit"},"Yes"),oe.default.createElement(g.Button,{variant:"outlined",type:"submit",onClick:t},"Cancel"))),u?oe.default.createElement(g.DialogContent,null,oe.default.createElement(g.DialogContentText,{color:"error"},u)):null)}function ut({handleClose:t,session:n}){const[a,o]=y.useState(),[r,i]=y.useState(""),{collaborationServerDriver:c,getInternetAccount:u,inMemoryFileDriver:d}=n.apolloDataStore,f=[...c.getAssemblies(),...d.getAssemblies()];return oe.default.createElement(Me,{open:!0,title:"Export GFF3",handleClose:t,maxWidth:!1,"data-testid":"download-gff3"},oe.default.createElement("form",{onSubmit:async function(o){if(o.preventDefault(),i(""),!a)return void i("Must select assembly to download");const{internetAccountConfigId:r}=e.getConf(a,["sequence","metadata"]);r?await async function(e){if(!a)return void i("Must select assembly to download");const t=u(a.configuration.name,e),n=new URL("export/getID",t.baseURL),o=new URLSearchParams({assembly:a.name});n.search=o.toString();const r=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:r}),l=await s(r,{method:"GET"});if(!l.ok){const e=await De(l,"Error when exporting ID");return void i(e)}const{exportID:c}=await l.json(),d=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c});d.search=f.toString();const g=d.toString();window.open(g,"_blank")}(r):function(t){if(!a)return void i("Must select assembly to download");const{assemblies:n}=t.apolloDataStore,o=n.get(a.name),r=o?.refSeqs;if(!r)return void i(`No refSeqs found for assembly "${a.name}"`);const 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e=r?-1:1,[n,a]=y*e==1?[wn,Sn]:[Sn,wn];t.fillStyle=n,t.fillRect(l+1,f+1,i-2,(g-2)/2),t.fillStyle=a,t.fillRect(l+1,f+(g-2)/2,i-2,(g-2)/2)}}w+=1}if(b)if(m===b._id){const e=n.length/u,s=r?a-e:a,i=o*d,l=this.getRowCount(n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,0.08)",t.fillRect(s,i,e,l)}else{let e,n,s=0;for(const[,t]of h??new Map)t._id===b?._id&&(e=t,n=s),s++;if(void 0===e||void 0===n)return;const i=this.cdsCount(e);let l=d;i>1&&(l*=i);const f=e.length/u,g=r?a-f:a+(e.start-p)/u,m=(o+n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,08)",t.fillRect(g,m,f,l)}}cdsCount(e){let t=0;for(const[,n]of e?.children??new Map)"CDS"===n.type&&n.discontinuousLocations&&n.discontinuousLocations.length>0&&t++;return t}drawHover(e,t,n,a,o){const{apolloHover:r}=e;if(!r)return;const{feature:s}=r;if(s)if(s.discontinuousLocations&&s.discontinuousLocations.length>0)for(const n of s.discontinuousLocations)this.drawShadeForFeature(e,t,n.start,n.end,n.end-n.start);else this.drawShadeForFeature(e,t,s.start,s.end,s.length,n,a,o)}drawShadeForFeature(e,t,n,a,o,r,s,i){const{apolloHover:l,apolloRowHeight:c,displayedRegions:u,lgv:d,theme:f}=e,{bpPerPx:g,bpToPx:m,offsetPx:h}=d;if(!l)return;const{feature:p,topLevelFeature:y}=l;if(!p||!y)return;let b,w,S,v=0;for(const[,e]of y.children??new Map){e._id===p?._id&&(b=e,S=v);for(const[,t]of e.children??new Map)t._id===p._id&&(w=t,b=e,S=v);v++}const C=this.cdsCount(b);if(C>1&&r&&s){if(void 0===b||void 0===S)return;const e=w?w.length/g:b.length/g,n=i?s-e:s+(w?(w.start-p.min)/g:(b.start-p.min)/g),a=(r+S)*c;t.fillStyle=f?.palette.action.selected??"rgba(0,0,0,04)",t.fillRect(n,a,e,c*C)}else{const{mousePosition:e}=l;if(!e)return;const r=c,{regionNumber:s,y:i}=e,d=Math.floor(i/r),p=u[s],{refName:y,reversed:b}=p,w=(m({refName:y,coord:b?a:n,regionNumber:s})?.offsetPx??0)-h,S=d*r,v=o/g;t.fillStyle=f?.palette.action.focus??"rgba(0,0,0,0.04)",t.fillRect(w,S,v,r)}}drawDragPreview(e,t){const{apolloDragging:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e,{bpPerPx:i,offsetPx:l}=r;if(!n)return;const{discontinuousLocation:c,feature:u,glyph:d,mousePosition:f}=n.start;if(!u)throw new Error("no feature for drag preview??");if(d!==this)throw new Error("drawDragPreview() called on wrong glyph?");const{mousePosition:m}=n.current,h=this.isMouseOnFeatureEdge(f,u,e);if(!h)return;const p=Math.floor(f.y/a),y=o[f.regionNumber];let b;b=c?y.reversed?y.end-c[h]:c[h]-y.start:y.reversed?y.end-u[h]:u[h]-y.start;const w=b/i-l,S=Math.min(m.x,w),v=p*a,C=Math.abs(m.x-w),E=1*a;t.strokeStyle=s?.palette.info.main??"rgb(255,0,0)",t.setLineDash([6]),t.strokeRect(S,v,C,E),t.fillStyle=g.alpha(s?.palette.info.main??"rgb(255,0,0)",.2),t.fillRect(S,v,C,E)}isMouseOnFeatureEdge(e,t,n,a){if(!e)return;const{bp:o,refName:r,regionNumber:s,x:i}=e,{lgv:l}=n,{bpToPx:c,offsetPx:u}=l;let d,f;if(t.discontinuousLocations&&t.discontinuousLocations.length>0){let e;for(const n of t.discontinuousLocations)if(o>=n.start&&o<=n.end){e=n;break}if(!e)return;d=c({refName:r,coord:e.start,regionNumber:s}),f=c({refName:r,coord:e.end,regionNumber:s})}else d=c({refName:r,coord:t.start,regionNumber:s}),f=c({refName:r,coord:t.end,regionNumber:s});if(void 0!==d&&void 0!==f){const e=d.offsetPx-u,n=f.offsetPx-u;if(Math.abs(n-e)<8)return;const o=this.getParentFeature(t,a);if(o){if("gene"===o.type)return;if(t.start<=o.start&&Math.abs(e-i)<4)return;if(t.end>=o.end&&Math.abs(n-i)<4)return}if(Math.abs(e-i)<4)return"start";if(Math.abs(n-i)<4)return"end"}}onMouseMove(e,t){const{feature:n,mousePosition:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);e.apolloDragging?e.setCursor("col-resize"):n&&a&&(this.isMouseOnFeatureEdge(a,n,e,o)?e.setCursor("col-resize"):e.setCursor())}onMouseDown(e,t){const{feature:n,mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);n&&a&&this.isMouseOnFeatureEdge(a,n,e)&&t.stopPropagation()}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}startDrag(e){const{feature:t,mousePosition:n,topLevelFeature:a}=e.apolloDragging?.start??{},{mousePosition:o}=e.apolloDragging?.current??{};return!!(t&&n&&o&&this.isMouseOnFeatureEdge(n,t,e,a))}adjacentExonsOfCdsDL(e,t){let n,a,o,r;if(t){for(const[n,a]of t.entries()){const t=a.cdsDL;if(e.start===t?.start&&e.end===t.end&&e.phase===t.phase){r=n;break}}if(void 0!==r){const{exon:e}=t[r];o=e}void 0!==r&&r>0&&(n=t[r-1].exon),void 0!==r&&r<t.length-1&&(a=t[r+1].exon)}return{prevExon:n,matchingExon:o,nextExon:a}}exonCDSRelation(e,t){const n=[];if(!e)return n;const a=this.getParentFeature(e,t);if(!a?.children)return n;for(const[,t]of a.children)if("exon"===t.type){const a=this.cdsDLForExon(t,e);n.push({exon:t,cdsDL:a?{start:a.start,end:a.end,phase:a.phase}:void 0})}return n}cdsDLForExon(e,t){let n;if(t.discontinuousLocations&&t.discontinuousLocations.length>0)for(const a of t.discontinuousLocations)if(a.start>=e.start&&a.end<=e.end){n=a;break}return n}cdsDlsForExon(e,t){const n=[],a=this.getParentFeature(e,t);if(!a?.children||!t)return n;const o=[];for(const[,e]of a.children)"CDS"===e.type&&o.push(e);for(const t of o)for(const[,o]of a.children)if("exon"===o.type&&o._id===e._id){const e=this.cdsDLForExon(o,t);e&&n.push(e)}return n}adjacentExonsOfExon(e,t){const n=this.getParentFeature(e,t);if(!n||!n.children)return;let a,o,r=0;for(const[,t]of n.children){if(t._id===e._id)break;r++}const s=[...n.children.keys()];if(r>0){const e=n.children.get(s[r-1]);e&&"exon"===e.type&&(a=e)}if(r<s.length-1){const e=n.children.get(s[r+1]);e&&"exon"===e.type&&(o=e)}return{prevExon:a,nextExon:o}}continueDrag(e,t){const{discontinuousLocation:n,feature:a,glyph:o,mousePosition:r,topLevelFeature:s}=e.apolloDragging?.start??{};if(!t||!r)return;const{bp:i}=t;if(!a||!t)return;const l=this.isMouseOnFeatureEdge(r,a,e,s);if("CDS"===a.type&&a.discontinuousLocations&&a.discontinuousLocations.length>0&&n){const e=this.exonCDSRelation(a,s),{matchingExon:t,nextExon:o,prevExon:r}=this.adjacentExonsOfCdsDL(n,e);if(o&&i>=o.start-1)return;if(r&&i<=r.end+1)return;if(!r&&o&&t&&i<t.start)return;if(r&&!o&&t&&i>t.end)return;if(l&&("start"===l&&i>=n.end-1||"end"===l&&i<=n.start+1))return}if("CDS"!==a.type){const e=this.adjacentExonsOfExon(a,s);if(e?.nextExon&&i>=e?.nextExon.start-1)return;if(e?.prevExon&&i<=e?.prevExon.end+1)return;const t=this.cdsDlsForExon(a,s);if(t&&t.length>0){let e;for(const n of t)if(l&&("start"===l&&i>=n.start-1||"end"===l&&i<=n.end+1)){e=!0;break}if(e)return}else if(l&&("start"===l&&i>=a.end-1||"end"===l&&i<=a.start+1))return}e.setDragging({start:{feature:a,topLevelFeature:s,glyph:o,discontinuousLocation:n,mousePosition:r},current:{feature:a,topLevelFeature:s,glyph:o,mousePosition:t}})}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];let o;for(const e of a)void 0!==e.start&&void 0!==e.end&&void 0!==e.phase?t>=e.start&&t<=e.end&&e.parent&&(o=e.annotationFeature):t>=e.annotationFeature.start&&t<=e.annotationFeature.end&&e.parent&&(o=e.annotationFeature);return o||(o=a.at(-1)?.annotationFeature),o}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e.annotationFeature._id===t._id)))return e}async executeDrag(e){const{apolloDragging:t,changeManager:n,displayedRegions:a,getAssemblyId:o,setCursor:r}=e;if(!t)return;const{discontinuousLocation:s,feature:i,glyph:l,mousePosition:c,topLevelFeature:u}=t.start;if(!i)throw new Error("no feature for drag preview??");if(l!==this)throw new Error("drawDragPreview() called on wrong glyph?");const d=this.isMouseOnFeatureEdge(c,i,e);if(!d)return;const{mousePosition:f}=t.current,g=f.bp,m=o(a[c.regionNumber].assemblyName),h=[];if("start"===d)if(void 0!==s?.idx&&i.discontinuousLocations&&i.discontinuousLocations.length>0){this.addDiscontinuousLocStartChange(h,i,g,i.discontinuousLocations[s.idx].start,m,s.idx);const e=this.exonCDSRelation(i,u),t=this.adjacentExonsOfCdsDL(s,e);t&&t.matchingExon&&g<t.matchingExon.start&&this.addStartLocationChange(h,t.matchingExon,g,m)}else this.addStartLocationChange(h,i,g,m);else if(void 0!==s?.idx&&i.discontinuousLocations&&i.discontinuousLocations.length>0){this.addDiscontinuousLocEndChange(h,i,g,i.discontinuousLocations[s.idx].end,m,s.idx);const e=this.exonCDSRelation(i,u),t=this.adjacentExonsOfCdsDL(s,e);t&&t.matchingExon&&g>t.matchingExon.end&&this.addEndLocationChange(h,t.matchingExon,g,m)}else this.addEndLocationChange(h,i,g,m);if(!n)throw new Error("no change manager");for(const e of h)await n.submit(e);r()}addDiscontinuousLocStartChange(e,t,n,a,o,r){e.push(new s.DiscontinuousLocationStartChange({typeName:"DiscontinuousLocationStartChange",changedIds:[t._id],featureId:t._id,newStart:n,oldStart:a,index:r,assembly:o}))}addDiscontinuousLocEndChange(e,t,n,a,o,r){e.push(new s.DiscontinuousLocationEndChange({typeName:"DiscontinuousLocationEndChange",changedIds:[t._id],featureId:t._id,newEnd:n,oldEnd:a,index:r,assembly:o}))}addEndLocationChange(e,t,n,a){const o=t._id;e.push(new s.LocationEndChange({typeName:"LocationEndChange",changedIds:[o],featureId:o,oldEnd:t.end,newEnd:n,assembly:a}))}addStartLocationChange(e,t,n,a){const o=t._id;e.push(new s.LocationStartChange({typeName:"LocationStartChange",changedIds:[o],featureId:o,oldStart:t.start,newStart:n,assembly:a}))}},Fn=new class extends bn{featuresForRow(e){const t=[[e]];if(e.children)for(const[,n]of e.children??new Map)t.push(...this.featuresForRow(n));return t}getRowCount(e){return this.featuresForRow(e).length}draw(e,t,n,a,o,r){for(let s=0;s<this.getRowCount(n);s++)this.drawRow(e,t,n,a,o+s,o,r)}drawRow(e,t,n,a,o,r,s){const i=this.featuresForRow(n)[o-r];for(const r of i)this.drawFeature(e,t,n,r,a,o,s)}drawFeature(e,t,n,a,o,r,s){const{apolloRowHeight:i,lgv:l,session:c}=e,{bpPerPx:u}=l,{apolloSelectedFeature:d}=c,f=(a.start-n.min)/u,g=a.length/u,m=s?o-f-g:o+f,h=r*i,p=this.getRowCount(a),y=this.getIsSelectedFeature(a,d);p>1&&this.drawBox(t,m,h,g,p*i,y?"rgba(130,0,0,0.45)":"rgba(255,0,0,0.25)"),super.draw(e,t,a,m,r,s)}drawHover(e,t){const{apolloHover:n,apolloRowHeight:a,displayedRegions:o,lgv:r}=e;if(!n)return;const{feature:s,mousePosition:i}=n;if(!s||!i)return;const{regionNumber:l,y:c}=i,u=o[l],{refName:d,reversed:f}=u,{bpPerPx:g,bpToPx:m,offsetPx:h}=r,{end:p,length:y,start:b}=s,w=(m({refName:d,coord:f?p:b,regionNumber:l})?.offsetPx??0)-h,S=Math.floor(c/a)*a,v=y/g;t.fillStyle="rgba(0,0,0,0.2)",t.fillRect(w,S,v,a*this.getRowCount(s))}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}continueDrag(e,t){}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];return a?.find((e=>t>=e.start&&t<=e.end))}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e._id===t._id)))return e}},An=new class extends yn{featuresForRow(e){const t=[];for(const[,n]of e.children??new Map){const e=[];for(const[,t]of n.children??new Map)e.push(t);e.push(n),t.push(e)}return t}getRowCount(e){let t=0;for(const[,n]of e.children??new Map)"mRNA"===n.type&&(t+=1);return t}draw(e,t,n,a,o,r){const{apolloRowHeight:s,lgv:i,session:l,theme:c}=e,{bpPerPx:u}=i,d=s,f=Math.round(.6*d),g=Math.round(.9*d),{_id:m,children:h,min:p,strand:y}=n,{apolloSelectedFeature:b}=l;let w=0;for(const[,e]of h??new Map){if("mRNA"!==e.type)continue;const n=(e.start-p)/u,s=e.length/u,i=r?a-n-s:a+n,l=Math.round((w+.5)*d)+o*d;t.strokeStyle=c?.palette.text.primary??"black",t.beginPath(),t.moveTo(i,l),t.lineTo(i+s,l),t.stroke(),w+=1}w=0;for(const[,e]of h??new Map){if("mRNA"!==e.type)continue;const n=[...e.children??[]].filter((([,e])=>"CDS"===e.type)).length;for(let s=0;s<n;s++)for(const[,n]of e.children??new Map){const e="CDS"===n.type,s=n.type.endsWith("UTR");if(!e&&!s)continue;const i=(n.start-p)/u,l=n.length/u,m=r?a-i-l:a+i;t.fillStyle=c?.palette.text.primary??"black";const h=e?g:f,S=(o+w)*d+(d-h)/2;if(t.fillRect(m,S,l,h),l>2&&(t.clearRect(m+1,S+1,l-2,h-2),t.fillStyle=b&&n._id===b._id?"rgb(0,0,0)":e?"rgb(171,71,188)":"rgb(211,211,211)",t.fillRect(m+1,S+1,l-2,h-2),vn&&Cn&&y)){const e=r?-1:1,[n,a]=y*e==1?[vn,Cn]:[Cn,vn];t.fillStyle=n,t.fillRect(m+1,S+1,l-2,(h-2)/2),t.fillStyle=a,t.fillRect(m+1,S+1+(h-2)/2,l-2,(h-2)/2)}}w+=1}if(b)if(m===b._id){const e=n.length/u,s=r?a-e:a,i=o*d,l=this.getRowCount(n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,0.08)",t.fillRect(s,i,e,l)}else{let e,n,s=0;for(const[,t]of h??new Map)t._id===b?._id&&(e=t,n=s),s++;if(void 0===e||void 0===n)return;const i=e.length/u,l=r?a-i:a+(e.start-p)/u,f=(o+n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,08)",t.fillRect(l,f,i,d)}}drawHover(e,t){const{apolloHover:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e;if(!n)return;const{feature:i,mousePosition:l}=n;if(!i||!l)return;const{regionNumber:c,y:u}=l,{bpPerPx:d,bpToPx:f,offsetPx:g}=r,m=a,h=Math.floor(u/m),p=o[c],{refName:y,reversed:b}=p,w=(f({refName:y,coord:b?i.end:i.start,regionNumber:c})?.offsetPx??0)-g,S=h*m,v=i.length/d;t.fillStyle=s?.palette.action.focus??"rgba(0,0,0,0.04)",t.fillRect(w,S,v,m)}drawDragPreview(e,t){const{apolloDragging:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e,{bpPerPx:i,offsetPx:l}=r;if(!n)return;const{feature:c,glyph:u,mousePosition:d}=n.start;if(!c)throw new Error("no feature for drag preview??");if(u!==this)throw new Error("drawDragPreview() called on wrong glyph?");const{mousePosition:f}=n.current,m=this.isMouseOnFeatureEdge(d,c,e);if(!m)return;const h=Math.floor(d.y/a),p=o[d.regionNumber],y=(p.reversed?p.end-c[m]:c[m]-p.start)/i-l,b=Math.min(f.x,y),w=h*a,S=Math.abs(f.x-y),v=1*a;t.strokeStyle=s?.palette.info.main??"rgb(255,0,0)",t.setLineDash([6]),t.strokeRect(b,w,S,v),t.fillStyle=g.alpha(s?.palette.info.main??"rgb(255,0,0)",.2),t.fillRect(b,w,S,v)}isMouseOnFeatureEdge(e,t,n,a){if(!e)return;const{refName:o,regionNumber:r,x:s}=e,{lgv:i}=n,{bpToPx:l,offsetPx:c}=i,u=l({refName:o,coord:t.start,regionNumber:r}),d=l({refName:o,coord:t.end,regionNumber:r});if(void 0!==u&&void 0!==d){const e=u.offsetPx-c,n=d.offsetPx-c;if(Math.abs(n-e)<8)return;const o=this.getParentFeature(t,a);if(o&&t.start<=o.start&&Math.abs(e-s)<4)return;if(o&&t.end>=o.end&&Math.abs(n-s)<4)return;if(Math.abs(e-s)<4)return"start";if(Math.abs(n-s)<4)return"end"}}onMouseMove(e,t){const{feature:n,mousePosition:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);e.apolloDragging?e.setCursor("col-resize"):n&&a&&(this.isMouseOnFeatureEdge(a,n,e,o)?e.setCursor("col-resize"):e.setCursor())}onMouseDown(e,t){const{feature:n,mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);n&&a&&this.isMouseOnFeatureEdge(a,n,e)&&t.stopPropagation()}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}startDrag(e){const{feature:t,mousePosition:n,topLevelFeature:a}=e.apolloDragging?.start??{},{mousePosition:o}=e.apolloDragging?.current??{};return!!(t&&n&&o&&this.isMouseOnFeatureEdge(n,t,e,a))}continueDrag(e,t){const{feature:n,glyph:a,mousePosition:o,topLevelFeature:r}=e.apolloDragging?.start??{};if(!t||!o)return;const s=this.getParentFeature(n,r),i=this.getAdjacentFeatures(n,s);if(!n||!t)return;const{bp:l}=t,c=this.isMouseOnFeatureEdge(o,n,e,r);if(!c||!("start"===c&&l>=n.end-1||"end"===c&&l<=n.start+1)){if("CDS"!==n.type){if(i.prevFeature&&!i.nextFeature){if("CDS"===i.prevFeature.type&&l<=i.prevFeature.start+1)return;if("CDS"!==i.prevFeature.type&&l<=i.prevFeature.end+1)return}if(!i.prevFeature&&i.nextFeature){if("CDS"===i.nextFeature.type&&l>=i.nextFeature.end-1)return;if("CDS"!==i.nextFeature.type&&l>=i.nextFeature.start-1)return}}if(i.prevFeature&&i.nextFeature)if("CDS"===n.type){if("CDS"!==i.nextFeature.type&&l>=i.nextFeature.end-1)return;if("CDS"===i.nextFeature.type&&l>=i.nextFeature.start-1)return;if("CDS"!==i.prevFeature.type&&l<=i.prevFeature.start+1)return;if("CDS"===i.prevFeature.type&&l<=i.prevFeature.end+1)return}else{if("CDS"===i.prevFeature.type&&l<=i.prevFeature.start+1)return;if("CDS"!==i.prevFeature.type&&l<=i.prevFeature.end+1)return;if("CDS"!==i.nextFeature.type&&l>=i.nextFeature.start-1)return;if("CDS"===i.nextFeature.type&&l>=i.nextFeature.end-1)return}e.setDragging({start:{feature:n,topLevelFeature:r,glyph:a,mousePosition:o},current:{feature:n,topLevelFeature:r,glyph:a,mousePosition:t}})}}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];return a?.find((e=>t>=e.start&&t<=e.end))}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e._id===t._id)))return e}async executeDrag(e){const{apolloDragging:t,changeManager:n,displayedRegions:a,getAssemblyId:o,setCursor:r}=e;if(!t)return;const{feature:s,glyph:i,mousePosition:l,topLevelFeature:c}=t.start;if(!s)throw new Error("no feature for drag preview??");if(i!==this)throw new Error("drawDragPreview() called on wrong glyph?");const u=this.isMouseOnFeatureEdge(l,s,e);if(!u)return;const{mousePosition:d}=t.current,f=d.bp,g=o(a[l.regionNumber].assemblyName),m=this.getParentFeature(s,c),h=this.getAdjacentFeatures(s,m),p=[];if("end"===u){this.addEndLocation(p,s,f,g);const{nextFeature:e}=h;if(!e)return;("CDS"!==s.type&&"CDS"===e.type||"CDS"===s.type&&"CDS"!==e.type)&&this.addStartLocation(p,e,f+1,g)}else{this.addStartLocation(p,s,f,g);const{prevFeature:e}=h;if(!e)return;("CDS"!==s.type&&"CDS"===e.type||"CDS"===s.type&&"CDS"!==e.type)&&this.addEndLocation(p,e,f-1,g)}if(!n)throw new Error("no change manager");for(const e of p)await n.submit(e);r()}getAdjacentFeatures(e,t){let n,a,o=0;if(!e||!t||!t.children)return{prevFeature:n,nextFeature:a};for(const[,n]of t.children){if(n._id===e._id)break;o++}const r=[...t.children.keys()];return o>0&&(n=t.children.get(r[o-1])),o<r.length-1&&(a=t.children.get(r[o+1])),{prevFeature:n,nextFeature:a}}addEndLocation(e=[],t,n,a){const o=t._id;e.push(new s.LocationEndChange({typeName:"LocationEndChange",changedIds:[o],featureId:o,oldEnd:t.end,newEnd:n,assembly:a}))}addStartLocation(e=[],t,n,a){const o=t._id;e.push(new s.LocationStartChange({typeName:"LocationStartChange",changedIds:[o],featureId:o,oldStart:t.start,newStart:n,assembly:a}))}};function Dn(e,t){if("gene"===e.type){let t=!1;for(const[,n]of e.children??new Map)if("mRNA"===n.type)for(const[,e]of n.children??new Map)"exon"===e.type&&(t=!0);return t?xn:An}return e.children?.size?Fn:En}const kn=l.types.model({heightPreConfig:l.types.maybe(l.types.refinement("displayHeight",l.types.number,(e=>e>=20)))}).volatile((()=>({scrollTop:0}))).views((t=>({get height(){return t.heightPreConfig??e.getConf(t,"height")}}))).actions((e=>({setScrollTop(t){e.scrollTop=t},setHeight:t=>(e.heightPreConfig=Math.max(t,20),e.height),resizeHeight(t){const n=e.height;return this.setHeight(e.height+t)-n}})));function Mn(e,t){return t?.palette.bases[e.toUpperCase()].main.toString()??"lightgray"}function Rn(e,t,n,a,o){const r=Math.min(n,10);e.fillStyle="#000",e.font=`${r}px`;const s=e.measureText(a).width;e.fillText(a,t+(n-s)/2,o+10)}function Ln(e,t,n,o,r,s,i,l,c){let u=i.slice(l,l+3).toUpperCase();c&&(u=function(e){return[...e].map((e=>a.revcom(e))).reverse().join("")}(u));const d=a.defaultCodonTable[u];var f;d&&(e.beginPath(),e.fillStyle=(f=d,{M:"#33ee33","*":"#f44336"}[f?.toUpperCase()]||"lightgray"),e.rect(n,o,r,s),e.fill(),t<=.1&&(e.stroke(),Rn(e,n,r,d,o)))}function Nn(e,t){return"CDS"===e.type&&void 0!==e.phase?-1===e.strand?(e.end-e.phase)%3+(t<=1?5:3):Math.abs((e.start+e.phase)%3-2):t<=1?-1===e.strand?4:3:void 0}function Tn(e,t,n,a,o,r){void 0!==o&&(e.fillStyle=t?.palette.action.focus??"rgba(0,0,0,0.04)",e.fillRect(n,a*o,r,a))}function In(n,o){return function(n,o){const r=function(n,o){return function(n,o){const r=function(n,o){return function(n,o){const r=function(n,o){return function(n,o){const r=function(n,o){return l.types.compose(t.BaseDisplay,kn).named("BaseLinearApolloDisplay").props({type:l.types.literal("LinearApolloDisplay"),configuration:e.ConfigurationReference(o)}).volatile((e=>({lgv:a.getContainingView(e)}))).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...G.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get session(){return a.getSession(e)},get regions(){return e.lgv.dynamicBlocks.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:Math.round(a),end:Math.round(t)})))},get displayedRegions(){return e.lgv.displayedRegions},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>=200)return"Zoom in to see annotations"}}))).views((t=>({get apolloInternetAccount(){const[n]=t.regions,{internetAccounts:a}=l.getRoot(t),{assemblyName:o}=n,{assemblyManager:r}=t.session,s=r.get(o);if(!s)throw new Error(`No assembly found with name 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o=t.get(n.assemblyName);let r,s;const{end:i,refName:l,start:c}=n;for(const[,t]of e.seenFeatures)l!==o?.getCanonicalRefName(t.refSeq)||!a.doesIntersect2(c,i,t.min,t.max)||t.length>e.featuresMinMaxLimit||(void 0===r&&({min:r}=t),void 0===s&&({max:s}=t),t.min<r&&({min:r}=t),t.end>s&&({max:s}=t));if(void 0!==r&&void 0!==s)return[r,s]}))}}))).actions((e=>({addSeenFeature(t){e.seenFeatures.set(t._id,t)},deleteSeenFeature(t){e.seenFeatures.delete(t)}}))).views((e=>({get featureLayouts(){const{assemblyManager:t}=e.session;return e.displayedRegions.map(((n,o)=>{const r=t.get(n.assemblyName),s=new Map,i=e.featuresMinMax[o];if(!i)return s;const[c,u]=i,d=[],{end:f,refName:g,start:m}=n;for(const[t,n]of e.seenFeatures.entries()){if(!l.isAlive(n)){e.deleteSeenFeature(t);continue}if(g!==r?.getCanonicalRefName(n.refSeq)||!a.doesIntersect2(m,f,n.min,n.max))continue;const o=Dn(n).getRowCount(n,e.lgv.bpPerPx);let i=0,h=!1;for(;!h;){let e=d.slice(i,i+o);if(e.length<o){for(let t=0;t<o-e.length;t++){const e=d.length;d[e]=Array.from({length:u-c}),s.set(e,[])}e=d.slice(i,i+o)}if(e.map((e=>{const t=n.max-n.min==0?n.min+1:n.max;let a=n.min-c,o=t-c;return n.min-c<0&&(a=0,o=t-n.min),e.slice(a,o).some(Boolean)})).some(Boolean))i+=1;else{for(let e=i;e<i+o;e++){let t=n.min-c,a=n.max-c;n.min-c<0&&(t=0,a=n.max-n.min),d[e].fill(!0,t,a);const o=s.get(e);o?.push([e-i,n])}h=!0}}}return s}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const n of t)for(const[t,a]of n)for(const[n,o]of a)if(0===n){if(e._id===o._id)return{layoutRow:t,featureRow:n};if(o.hasDescendant(e._id)){const n=Dn(o).getRowForFeature(o,e);if(void 0!==n)return{layoutRow:t,featureRow:n}}}}}))).views((e=>({get highestRow(){return Math.max(0,...e.featureLayouts.map((e=>Math.max(...e.keys()))))}}))).actions((e=>({afterAttach(){l.addDisposer(e,i.autorun((()=>{if(e.lgv.initialized&&!e.regionCannotBeRendered())for(const t of e.regions){const n=e.session.apolloDataStore.assemblies.get(t.assemblyName),o=n?.getByRefName(t.refName);for(const[,n]of o?.features??new Map)a.doesIntersect2(t.start,t.end,n.start,n.end)&&!e.seenFeatures.has(n._id)&&e.addSeenFeature(n)}}),{name:"LinearApolloDisplaySetSeenFeatures",delay:1e3}))}})))}(0,o).named("LinearApolloDisplayRendering").props({sequenceRowHeight:15,apolloRowHeight:20,detailsMinHeight:200,detailsHeight:200,lastRowTooltipBufferHeight:40,isShown:!0}).volatile((()=>({canvas:null,overlayCanvas:null,collaboratorCanvas:null,seqTrackCanvas:null,seqTrackOverlayCanvas:null,theme:void 0}))).views((e=>({get featuresHeight(){return(e.highestRow+1)*e.apolloRowHeight+e.lastRowTooltipBufferHeight}}))).actions((e=>({toggleShown(){e.isShown=!e.isShown},setDetailsHeight(t){e.detailsHeight=e.isShown?Math.max(Math.min(t,e.height-100),Math.min(e.height,e.detailsMinHeight)):t},setCanvas(t){e.canvas=t},setOverlayCanvas(t){e.overlayCanvas=t},setCollaboratorCanvas(t){e.collaboratorCanvas=t},setSeqTrackCanvas(t){e.seqTrackCanvas=t},setSeqTrackOverlayCanvas(t){e.seqTrackOverlayCanvas=t},setTheme(t){e.theme=t},afterAttach(){l.addDisposer(e,i.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.collaboratorCanvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);for(const n of e.session.collaborators){const{locations:a}=n;if(0===a.length)continue;let o=0;for(const r of e.lgv.displayedRegions){for(const s of a){if(s.refSeq!==r.refName)continue;const{end:a,refSeq:i,start:l}=s,c=e.lgv.bpToPx({refName:i,coord:l,regionNumber:o});if(!c)continue;const u=c.offsetPx-e.lgv.offsetPx,d=(a-l)/e.lgv.bpPerPx;t.fillStyle="rgba(0,255,0,.2)",t.fillRect(u,1,d,100),t.fillStyle="black",t.fillText(n.name,u+1,11,d-2)}o++}}}}),{name:"LinearApolloDisplayRenderCollaborators"}))}})))}(0,o);return r.actions((e=>({afterAttach(){l.addDisposer(e,i.autorun((async()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;if(e.lgv.bpPerPx>3)return;const t=e.seqTrackCanvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);for(const[n,o]of e.regions.entries()){const r=e.session.apolloDataStore.getBackendDriver(o.assemblyName);if(!r)throw new Error("Failed to get the backend driver");const{seq:s}=await r.getSequence(o);if(!s)return;for(const[r,i]of[...s].entries()){const l=(e.lgv.bpToPx({refName:o.refName,coord:o.start+r,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,c=3/e.lgv.bpPerPx,u=e.displayedRegions[n].reversed?l-c:l;for(let n=2;n>=0;n--)(o.start+r)%3===n&&Ln(t,e.lgv.bpPerPx,u,e.sequenceRowHeight*(2-n),c,e.sequenceRowHeight,s,r,!1);if(e.lgv.bpPerPx<=1){const s=(e.lgv.bpToPx({refName:o.refName,coord:o.start+r,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,l=1/e.lgv.bpPerPx,c=e.displayedRegions[n].reversed?s-l:s;t.beginPath(),t.fillStyle=Mn(i,e.theme),t.rect(c,3*e.sequenceRowHeight,l,e.sequenceRowHeight),t.fill(),e.lgv.bpPerPx<=.1&&(t.stroke(),Rn(t,c,l,i,3*e.sequenceRowHeight));const u=a.revcom(i);t.beginPath(),t.fillStyle=Mn(u,e.theme),t.rect(c,4*e.sequenceRowHeight,l,e.sequenceRowHeight),t.fill(),e.lgv.bpPerPx<=.1&&(t.stroke(),Rn(t,c,l,u,4*e.sequenceRowHeight))}for(let n=0;n<=2;n++)(o.start+r)%3===n&&Ln(t,e.lgv.bpPerPx,u,e.sequenceRowHeight*((e.lgv.bpPerPx<=1?5:3)+n),c,e.sequenceRowHeight,s,r,!0)}}}}),{name:"LinearApolloDisplayRenderSequence"}))}})))}(0,o).actions((e=>({afterAttach(){l.addDisposer(e,i.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.canvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);for(const[n,o]of e.featureLayouts.entries()){const r=e.displayedRegions[n];for(const[s,i]of o.entries())for(const[o,l]of i){if(o>0)continue;if(!a.doesIntersect2(r.start,r.end,l.min,l.max))continue;const i=(e.lgv.bpToPx({refName:r.refName,coord:l.min,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx;Dn(l).draw(e,t,l,i,s,r.reversed)}}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,o);return r.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0,apolloHover:null}))).views((e=>({getFeatureAndGlyphUnderMouse(t){const n=function(e,t){const n=e.currentTarget,{clientX:a,clientY:o}=e,{left:r,top:s}=n.getBoundingClientRect()||{left:0,top:0},i=a-r,l=o-s,{coord:c,index:u,refName:d}=t.pxToBp(i);return{x:i,y:l,refName:d,bp:c,regionNumber:u}}(t,e.lgv),{bp:a,regionNumber:o,y:r}=n,s=Math.floor(r/e.apolloRowHeight),i=e.featureLayouts[o].get(s);if(!i)return{mousePosition:n};const l=i.find((e=>a>=e[1].min&&a<=e[1].max));if(!l)return{mousePosition:n};const[c,u]=l,d=Dn(u);return{feature:d.getFeatureFromLayout(u,a,c),topLevelFeature:u,glyph:d,mousePosition:n}}}))).actions((e=>({continueDrag(t){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");t.stopPropagation();const{glyph:n}=e.apolloDragging.start,{mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);a&&n&&n.continueDrag(e,a)},setDragging(t){e.apolloDragging=t??null}}))).actions((e=>({setApolloHover(t){e.apolloHover=t},setCursor(t){e.cursor!==t&&(e.cursor=t)}}))).actions((()=>({onClick(){}})))}(0,o).actions((e=>({afterAttach(){l.addDisposer(e,i.autorun((async()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.seqTrackOverlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);const{apolloHover:n,displayedRegions:a,lgv:o,regions:r,sequenceRowHeight:s,theme:i}=e;if(!n)return;const{feature:l,mousePosition:c}=n;if(l&&c)for(const[e,n]of r.entries()){const r=Nn(l,o.bpPerPx);if(l.discontinuousLocations&&l.discontinuousLocations.length>0)for(const c of l.discontinuousLocations){const l=(o.bpToPx({refName:n.refName,coord:c.start,regionNumber:e})?.offsetPx??0)-o.offsetPx,u=(c.end-c.start)/o.bpPerPx;Tn(t,i,a[e].reversed?l-u:l,s,r,u)}else{const c=(o.bpToPx({refName:n.refName,coord:l.start,regionNumber:e})?.offsetPx??0)-o.offsetPx,u=l.length/o.bpPerPx;Tn(t,i,a[e].reversed?c-u:c,s,r,u)}}}),{name:"LinearApolloDisplayRenderSeqHighlight"}))}})))}(0,o);return r.views((e=>({contextMenuItems(t){const{apolloHover:n}=e,{topLevelFeature:a}=n??{};return a&&t?Dn(a).getContextMenuItems(e):[]}}))).actions((e=>({startDrag(t){const{feature:n,glyph:a,mousePosition:o,topLevelFeature:r}=e.getFeatureAndGlyphUnderMouse(t);if(n&&r&&a&&o){let s,i;if(n.discontinuousLocations&&n.discontinuousLocations.length>0)for(let e=0;e<n.discontinuousLocations.length;e++)if(o.bp>=n.discontinuousLocations[e].start&&o.bp<=n.discontinuousLocations[e].end){i=e,s=n.discontinuousLocations[i];break}e.apolloDragging={start:{glyph:a,feature:n,topLevelFeature:r,discontinuousLocation:s?{start:s.start,end:s.end,phase:s.phase,idx:i}:void 0,mousePosition:o},current:{glyph:a,feature:n,topLevelFeature:r,mousePosition:o}},a.startDrag(e,t)||(e.apolloDragging=null)}},endDrag(t){e.continueDrag(t),e.apolloDragging?.start.glyph?.executeDrag(e,t),e.setDragging()}}))).actions((e=>({onMouseDown(t){const{feature:n,glyph:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);a&&n&&o&&a.onMouseDown(e,t)},onMouseMove(t){const{buttons:n}=t,a=e.getFeatureAndGlyphUnderMouse(t),{glyph:o}=a;if(o&&o.onMouseMove(e,t),n)1===n&&(e.apolloDragging?e.continueDrag(t):e.startDrag(t));else{const{feature:t,topLevelFeature:n}=a;t&&o&&n?e.setApolloHover(a):(e.setApolloHover(null),e.setCursor())}},onMouseLeave(t){e.setDragging();const{glyph:n}=e.getFeatureAndGlyphUnderMouse(t);n&&n.onMouseLeave(e,t)},onMouseUp(t){const{glyph:n}=e.getFeatureAndGlyphUnderMouse(t);n&&n.onMouseUp(e,t),e.apolloDragging&&e.endDrag(t)}}))).actions((e=>({afterAttach(){l.addDisposer(e,i.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.overlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);const{apolloDragging:n,apolloHover:a,displayedRegions:o,featureLayouts:r,lgv:s}=e;if(!a)return;const{feature:i,glyph:l}=a;if(!i)return;let c=0,u=0,d=!1;for(const[e,t]of r.entries()){const n=o[e];for(const[a,o]of t.entries())if(0===c)for(const[,t]of o)for(const[,o]of t.children??new Map)if(0===c)if(u=(s.bpToPx({refName:n.refName,coord:i.min,regionNumber:e})?.offsetPx??0)-s.offsetPx,({reversed:d}=n),o._id!==i._id)for(const[,e]of o.children??new Map)0===c&&(e._id!==i._id||(c=a));else c=a}l?.drawHover(e,t,c,u,d),l?.drawTooltip(e,t),n&&n.start.glyph?.drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,o).props({tabularEditor:l.types.optional(pn,{})}).named("LinearApolloDisplay")}const Pn=v.makeStyles()((e=>({canvasContainer:{position:"relative",left:0},canvas:{position:"absolute",left:0},ellipses:{textOverflow:"ellipsis",overflow:"hidden"},avatar:{position:"absolute",color:e.palette.warning.light,backgroundColor:e.palette.warning.contrastText}}))),qn=S.observer((function(e){const t=g.useTheme(),{model:n}=e,{apolloRowHeight:o,contextMenuItems:r,cursor:s,featuresHeight:i,isShown:l,onMouseDown:c,onMouseLeave:u,onMouseMove:d,onMouseUp:f,regionCannotBeRendered:m,session:h,setCanvas:p,setCollaboratorCanvas:w,setOverlayCanvas:S,setSeqTrackCanvas:v,setSeqTrackOverlayCanvas:C,setTheme:E,tabularEditor:x}=n,{classes:F}=Pn(),A=a.getContainingView(n);y.useEffect((()=>E(t)),[t,E]);const[D,k]=y.useState(),[M,R]=y.useState([]),L=m();if(!l)return null;const{assemblyManager:N}=h;return oe.default.createElement(oe.default.Fragment,null,A.bpPerPx<=3?oe.default.createElement("div",{className:F.canvasContainer,style:{width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95}},oe.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),v(e)},width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95,className:F.canvas,"data-testid":"seqTrackCanvas"}),oe.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),C(e)},width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95,className:F.canvas,"data-testid":"seqTrackOverlayCanvas"})):null,oe.default.createElement("div",{className:F.canvasContainer,style:{width:A.dynamicBlocks.totalWidthPx,height:i},onContextMenu:e=>{if(e.preventDefault(),M.length>0)R([]);else{const t=[e.clientX,e.clientY];k(t),R(r(t))}}},L?oe.default.createElement(g.Alert,{severity:"warning",classes:{message:F.ellipses}},oe.default.createElement(g.Tooltip,{title:L},oe.default.createElement("div",null,L))):oe.default.createElement(oe.default.Fragment,null,oe.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),w(e)},width:A.dynamicBlocks.totalWidthPx,height:i,className:F.canvas,"data-testid":"collaboratorCanvas"}),oe.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),p(e)},width:A.dynamicBlocks.totalWidthPx,height:i,className:F.canvas,"data-testid":"canvas"}),oe.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),S(e)},width:A.dynamicBlocks.totalWidthPx,height:i,onMouseMove:d,onMouseLeave:u,onMouseDown:c,onMouseUp:f,onClick:()=>{x.showPane()},className:F.canvas,style:{cursor:s??"default"},"data-testid":"overlayCanvas"}),A.displayedRegions.flatMap(((e,t)=>{const r=N.get(e.assemblyName);return[...h.apolloDataStore.checkResults.values()].filter((t=>r?.isValidRefName(t.refSeq)&&r?.getCanonicalRefName(t.refSeq)===e.refName&&a.doesIntersect2(e.start,e.end,t.start,t.end))).map((a=>{const r=(A.bpToPx({refName:e.refName,coord:a.start,regionNumber:t})?.offsetPx??0)-A.offsetPx,[s]=a.ids;if(!s)return null;const{topLevelFeature:i}=s,l=parent?n.getFeatureLayoutPosition(i)?.layoutRow??0:0;return oe.default.createElement(g.Tooltip,{key:a._id,title:a.message},oe.default.createElement(g.Avatar,{className:F.avatar,style:{top:l*o,left:r,height:o,width:o}},oe.default.createElement(Ce.default,null)))}))})),oe.default.createElement(b.Menu,{open:M.length>0,onMenuItemClick:(e,t)=>{t(),R([])},onClose:()=>{R([])},TransitionProps:{onExit:()=>{R([])}},anchorReference:"anchorPosition",anchorPosition:D?{top:D[1],left:D[0]}:void 0,style:{zIndex:t.zIndex.tooltip},menuItems:M}))))})),_n=S.observer((function({model:e}){const{height:t}=e;return oe.default.createElement("div",{style:{position:"absolute",left:0,top:t/2,width:"100%"}},oe.default.createElement("hr",{style:{margin:0,top:0,color:"black"}}))})),Un=v.makeStyles()((e=>({shading:{background:z.alpha(e.palette.primary.main,.2),overflowY:"scroll",overflowX:"hidden"},details:{background:e.palette.background.paper},accordionControl:{height:12,width:"100%","&:hover":{background:e.palette.action.hover},display:"flex",alignItems:"center",justifyContent:"center"},accordionRoot:{background:e.palette.divider},resizeHandle:{width:"100%",height:4,position:"absolute",cursor:"row-resize",zIndex:100},expandIcon:{},title:{userSelect:"none"}}))),On=({onResize:e})=>{const{classes:t}=Un(),n=y.useCallback((t=>{t.stopPropagation(),t.preventDefault(),e(t.movementY)}),[e]),a=y.useCallback((e=>{e.stopPropagation(),e.preventDefault(),window.removeEventListener("mousemove",n),window.removeEventListener("mouseup",a),window.removeEventListener("mouseleave",a)}),[n]);return oe.default.createElement("div",{onMouseDown:e=>{e.stopPropagation(),window.addEventListener("mousemove",n),window.addEventListener("mouseup",a),window.addEventListener("mouseleave",a)},onClick:e=>{e.stopPropagation(),e.preventDefault()},className:t.resizeHandle})},Bn=S.observer((function({onClick:e,onResize:t,open:n,title:a}){const{classes:o}=Un();return oe.default.createElement("div",{className:o.accordionRoot},n&&t?oe.default.createElement(On,{onResize:t}):null,oe.default.createElement("div",{className:o.accordionControl,onClick:e},oe.default.createElement(n?Se.default:ve.default,{className:o.expandIcon}),a?oe.default.createElement(g.Typography,{className:o.title,variant:"caption",component:"span"},a):null))})),jn=S.observer((function({model:e,...t}){const{classes:n}=Un(),{height:a,isShown:o,selectedFeature:r,tabularEditor:s,toggleShown:i}=e,l=s.isShown?e.detailsHeight:0,c=o?a-l-24:0,u=y.useRef(null);return y.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,u)),[e,r]),oe.default.createElement("div",{className:n.details,style:{height:a}},oe.default.createElement(Bn,{open:o,title:"Graphical",onClick:i}),oe.default.createElement("div",{className:n.shading,ref:u,style:{height:c}},oe.default.createElement(qn,{model:e,...t})),oe.default.createElement(Bn,{title:"Table",open:s.isShown,onClick:s.togglePane,onResize:t=>{e.setDetailsHeight(e.detailsHeight-t)}}),oe.default.createElement("div",{style:{height:l}},oe.default.createElement(hn,{model:e})))})),$n=l.types.model("JobsManager",{}).views((e=>({get jobStatusWidget(){const{widgets:t}=a.getSession(e);let n=t.get("JobsList");return n||(n=a.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 o=a.getSession(e);if(a.isSessionModelWithWidgets(o)){o.showWidget(e.jobStatusWidget),e.jobStatusWidget.updateJobStatusMessage(t,n??"Aborted unexpectedly");const a=e.jobStatusWidget.jobs.findIndex((e=>e.name===t));e.jobStatusWidget.addAbortedJob({...e.jobStatusWidget.jobs[a]}),e.jobStatusWidget.removeJob(t),o.notify("Job aborted","info")}},runJob(t){const n=a.getSession(e);a.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=a.getSession(e);a.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 Gn{clientStore;constructor(e){this.clientStore=e}}class Hn{dataStore;constructor(e){this.dataStore=e}recentChanges=[];async submit(e,t={}){const{addToRecents:n=!0,submitToBackend:o=!0,updateJobsManager:i=!1}=t,l=a.getSession(this.dataStore),c=new AbortController,{jobsManager:u}=a.getSession(this.dataStore),d={name:`${e.typeName}`,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort()}};i&&u.runJob(d);const f=await s.validationRegistry.frontendPreValidate(e);if(!f.ok){const e=`Pre-validation failed: "${f.resultsMessages}"`;return i&&u.abortJob(d.name,e),void l.notify(e,"error")}try{await e.execute(this.dataStore)}catch(e){return i&&u.abortJob(d.name,String(e)),console.error(e),void l.notify(String(e),"error")}if((await s.validationRegistry.frontendPostValidate(e,this.dataStore)).ok||await this.revert(e),o){i&&u.update(d.name,"Submitting to driver");const{collaborationServerDriver:n,getBackendDriver:a}=this.dataStore,o=r.isAssemblySpecificChange(e)?a(e.assembly):n;let s;try{s=await o.submitChange(e,t)}catch(t){return i&&u.abortJob(d.name,String(t)),console.error(t),l.notify(String(t),"error"),void await this.revert(e,!1)}if(!s.ok){const t=`Post-validation failed: "${f.resultsMessages}"`;return i&&u.abortJob(d.name,t),l.notify(t,"error"),void await this.revert(e,!1)}e.notification&&l.notify(e.notification,"success")}n&&this.recentChanges.push(e),i&&u.done(d)}async revert(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async revertLastChange(){const e=this.recentChanges.pop();if(e)return this.revert(e);a.getSession(this.dataStore).notify("No changes to undo!","warning")}}class Wn extends Gn{inFlight=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:a}=n,o=new URL("features/searchFeatures",a),r=new URLSearchParams({assemblies:t.join(","),term:e});o.search=r.toString();const s=o.toString(),i=await this.fetch(n,s);if(!i.ok){const e=await De(i,"searchFeatures failed");throw new Error(e)}return i.json()}async getFeatures(t){const{assemblyName:n,end:o,refName:r,start:s}=t,{assemblyManager:i}=a.getSession(this.clientStore),l=i.get(n);if(!l)throw new Error(`Could not find assembly with name "${n}"`);const{ids:c}=e.getConf(l,["sequence","metadata"]),u=c[r];if(!u)throw new Error(`Could not find refSeq "${r}"`);const d=this.clientStore.getInternetAccount(n),{baseURL:f}=d,g=new URL("features/getFeatures",f),m=new URLSearchParams({refSeq:u,start:String(s),end:String(o)});g.search=m.toString();const h=g.toString(),p=await this.fetch(d,h);if(!p.ok){const e=await De(p,"getFeatures failed");throw new Error(e)}return await this.checkSocket(n,r,d),p.json()}async checkSocket(e,t,n){const{socket:a}=n,o=n.retrieveToken(),s=`${e}-${t}`,i=new Hn(this.clientStore);a.hasListeners(s)||a.on(s,(async e=>{if(n.setLastChangeSequenceNumber(Number(e.changeSequence)),e.userSessionId!==o&&e.channel===s){const t=r.Change.fromJSON(e.changeInfo);await i.submit(t,{submitToBackend:!1})}}))}async getSequence(t){const n=`${t.refName}:${t.start}-${t.end}`,o=this.inFlight.get(n),{assemblyName:r,end:s,refName:i,start:l}=t,{assemblyManager:c}=a.getSession(this.clientStore),u=c.get(r);if(!u)throw new Error(`Could not find assembly with name "${r}"`);const{ids:d}=e.getConf(u,["sequence","metadata"]),f=d[i];if(!f)throw new Error(`Could not find refSeq "${i}"`);if(o)return{seq:await o,refSeq:f};let g=this.clientStore.assemblies.get(r);g||(g=this.clientStore.addAssembly(r));let m=g?.refSeqs.get(f);m||(m=g.addRefSeq(f,i));const h=m.getSequence(l,s);if(h.length===s-l)return{seq:h,refSeq:f};const p=this.clientStore.getInternetAccount(r),{baseURL:y}=p,b=new URL("sequence",y),w=new URLSearchParams({refSeq:f,start:String(l),end:String(s)});b.search=w.toString();const S=b.toString(),v=this.getSeqFromServer(p,S,m,l,s);this.inFlight.set(n,v);const C=await v;return await this.checkSocket(r,i,p),this.inFlight.delete(n),{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 getRegions(e){const{assemblyManager:t}=a.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:o}=n,r=new URL("refSeqs",o),s=new URLSearchParams({assembly:e});r.search=s.toString();const i=r.toString(),l=await this.fetch(n,i);if(!l.ok){let e;try{e=await l.text()}catch{e=""}throw new Error(`getRegions failed: ${l.status} (${l.statusText})${e?` (${e})`:""}`)}return(await l.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(t){const{assemblyManager:n}=a.getSession(this.clientStore);return n.assemblies.filter((n=>{const a=e.getConf(n,["sequence","metadata"]);return!(!(a&&a.apollo&&a.internetAccountConfigId)||t&&a.internetAccountConfigId!==t)}))}async submitChange(e,t={}){const{internetAccountId:n}=t,a=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,n),{baseURL:o}=a,r=new URL("changes",o).href,i=await this.fetch(a,r,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!i.ok){const e=await De(i,"submitChange failed");throw new Error(e)}const l=new s.ValidationResultSet;return i.ok||(l.ok=!1),l}}class zn extends Gn{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 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:t}=a.getSession(this.clientStore);return t.assemblies.filter((t=>{const n=e.getConf(t,["sequence","metadata"]);return Boolean(n&&n.apollo&&!n.file&&!n.internetAccountConfigId)}))}async submitChange(e,t={}){return new s.ValidationResultSet}async searchFeatures(e,t){return[]}}function Vn(e,t){const n=[];for(let a=0;a<e.length;a+=t){const o=e.slice(a,a+t);n.push(o)}return n}class Jn extends Gn{async loadAssembly(t){const{assemblyManager:n}=a.getSession(this.clientStore),o=n.get(t);if(!o)throw new Error(`Assembly ${t} not found`);const{file:r}=e.getConf(o,["sequence","metadata"]),s=require("node:fs");return xe(t,await s.promises.readFile(r,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}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 ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:t}=a.getSession(this.clientStore);return t.assemblies.filter((t=>{const n=e.getConf(t,["sequence","metadata"]);return Boolean(n&&n.apollo&&!n.internetAccountConfigId&&n.file)}))}async submitChange(t){if(!r.isAssemblySpecificChange(t))throw new Error(`Cannot use this type of change with local file: "${t.typeName}"`);const{assemblyManager:n}=a.getSession(this.clientStore),o=n.get(t.assembly);if(!o)throw new Error(`Could not find assembly with name "${t.assembly}"`);const{file:i}=e.getConf(o,["sequence","metadata"]),c=this.clientStore.assemblies.get(t.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${t.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 Fe(c);this.clientStore.addCheckResults(f);const g=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)g.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)g.push({comment:e});for(const[,e]of c.refSeqs){const{features:t}=e;for(const[,e]of t)g.push(s.makeGFF3Feature(l.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[t]=e.sequence,n=Vn(t.sequence,80).join("\n");g.push({id:e.name,description:e.description,sequence:n})}const m=Q.default.formatSync(g),h=require("node:fs");return await h.promises.writeFile(i,m,"utf8"),new s.ValidationResultSet}async searchFeatures(e,t){return[]}}function Xn(t,n){const o=new AbortController,{signal:r}=o,s=t.evaluateExtensionPoint("Apollo-extendAnnotationFeature",J.AnnotationFeature),c=function(t){const n=l.types.model("ClientDataStore",{typeName:l.types.optional(l.types.literal("Client"),"Client"),assemblies:l.types.map(J.ApolloAssembly),checkResults:l.types.map(J.CheckResult)}).views((e=>({get internetAccounts(){return l.getRoot(e).internetAccounts},get pluginConfiguration(){return l.getRoot(e).jbrowse.configuration.ApolloPlugin},getFeature:n=>l.resolveIdentifier(t,e.assemblies,n)}))).actions((e=>({addAssembly:t=>e.assemblies.put({_id:t,refSeqs:{}}),addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${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):l.getParentOfType(n,J.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 Hn(e),collaborationServerDriver:new Wn(e),inMemoryFileDriver:new zn(e),desktopFileDriver:a.isElectron?new Jn(e):void 0,ontologyManager:Ke.create()}))).actions((t=>({afterCreate(){const{ontologyManager:n,pluginConfiguration:a}=t,o=a.ontologies;for(const t of o||[]){const[a,o,r,s]=[e.readConfObject(t,"name"),e.readConfObject(t,"version"),e.readConfObject(t,"source"),e.readConfObject(t,"textIndexFields")];n.findOntology(a)||n.addOntology(a,o,r,{textIndexing:{indexFields:s}})}}}))).views((t=>({getBackendDriver(n){if(!n)return t.collaborationServerDriver;const o=a.getSession(t),{assemblyManager:r}=o,s=r.get(n);if(!s)return t.collaborationServerDriver;const{file:i,internetAccountConfigId:l}=e.getConf(s,["sequence","metadata"]);return a.isElectron&&i?t.desktopFileDriver:l?t.collaborationServerDriver:t.inMemoryFileDriver},getInternetAccount(n,o){if(!(n??o))throw new Error("Must provide either assemblyName or internetAccountId");let r=o;if(n&&!r){const{assemblyManager:o}=a.getSession(t),s=o.get(n);if(!s)throw new Error(`No assembly found with name ${n}`);({internetAccountConfigId:r}=e.getConf(s,["sequence","metadata"]))}const{internetAccounts:s}=t,i=s.find((e=>e.internetAccountId===r));if(!i)throw new Error(`No InternetAccount found with config id ${o}`);return i}}))).actions((e=>({loadFeatures:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:s}=n;let i=e.assemblies.get(r);i||(i=e.assemblies.put({_id:r,refSeqs:{}}));const[l]=a;let c=i.refSeqs.get(l.refSeq);c||(c=i.refSeqs.put({_id:l.refSeq,name:s,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:s,refName:i,start:l}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:i,sequence:[]})),u.addSequence({start:l,stop:s,sequence:o})}}))})));return l.types.snapshotProcessor(n,{postProcessor:e=>(e.assemblies={},e.checkResults={},e)})}(s);return n.props({apolloDataStore:l.types.optional(c,{typeName:"Client"}),apolloSelectedFeature:l.types.safeReference(s),jobsManager:l.types.optional($n,{})}).extend((()=>{const e=i.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((t=>({apolloSetSelectedFeature(e){t.apolloSelectedFeature=e},addApolloTrackConfig(n,a){const o=`apollo_track_${n.name}`;t.tracks.some((e=>e.trackId===o))||t.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${e.getConf(n,"displayName")||n.name})`,assemblyNames:[n.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[n.name],textSearchAdapterId:`apollo_search_${n.name}`,...a?{baseURL:{uri:a,locationType:"UriLocation"}}:{}}},displays:[{type:"LinearApolloDisplay",displayId:`${o}-LinearApolloDisplay`},{type:"SixFrameFeatureDisplay",displayId:`${o}-SixFrameFeatureDisplay`}]})},broadcastLocations(){const{internetAccounts:e}=l.getRoot(t),n=[];for(const e of t.views){if("LinearGenomeView"!==e.type)return;const t=e;if(t.initialized){const{dynamicBlocks:e}=t;e.forEach((e=>{if(void 0!==e.regionNumber){const{assemblyName:t,end:a,refName:o,start:r}=e;n.push({assemblyName:t,refName:o,start:r,end:a})}}))}}if(0===n.length){for(const t of e)"baseURL"in t&&t.postUserLocation([]);return}const a=[];for(const t of e)if("baseURL"in t){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});t.postUserLocation(a)}}}))).actions((e=>({afterCreate:l.flow((function*(){const{internetAccounts:t}=l.getRoot(e);i.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const e=t;if(e.initialized){const{dynamicBlocks:t}=e;t.forEach((e=>{if(void 0!==e.regionNumber){const{assemblyName:t,end:a,refName:o,start:r}=e;n.push({assemblyName:t,refName:o,start:r,end:a})}}))}}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 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r.named("SixFrameFeatureDisplay").props({type:l.types.literal("SixFrameFeatureDisplay"),configuration:e.ConfigurationReference(n),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=a.getContainingView(e);if(t&&t.bpPerPx>=200)return"Zoom in to see annotations"},get session(){return a.getSession(e)}}))).actions((e=>{let t=[];return{afterAttach(){l.addDisposer(e,i.autorun((()=>{const n=a.getSession(e);if(a.getContainingView(e).initialized){if(e.regionCannotBeRendered())return;const a=[],o=[];for(const n of 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Map,o.set(e.refName,r));for(const[t,n]of a?.features.entries()??new Map)e.start<n.end&&e.end>n.start&&r.set(t,n)}return o},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.end>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 o=0;o<6;o++){const r=[],s=[],i=o in Zn;let l,c,u;i?(l=(t.length+n)%3,c=(Zn[o]+l+3)%3,u=a.reverse(t).slice(c)):(l=3-n%3,c=(Yn[o]+l+3)%3,u=t.slice(c));for(let e=0;e<u.length;e+=3){const t=u.slice(e,e+3),o=i?a.reverse(a.revcom(t)):t,l=i?n+u.length-(3+e):n+e+c;a.defaultStarts.includes(o.toUpperCase())?r.push(l):a.defaultStops.includes(o.toUpperCase())&&s.push(l)}e.set(o,{starts:r,stops:s})}return e},get featureLayout(){const e=new Map;for(const[t,n]of this.features||[]){if(!n)continue;const 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a.getSession(e).apolloSetSelectedFeature}}))).actions((e=>({setSelectedFeature:t=>a.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 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a=e.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:t.createBaseTrackConfig(n),explicitIdentifier:"trackId"});return new t.TrackType({name:"ApolloTrack",configSchema:a,stateModel:t.createBaseTrackModel(n,"ApolloTrack",a)})})),n.addInternetAccountType((()=>new t.InternetAccountType({name:"ApolloInternetAccount",configSchema:Ee,stateModel:Pt(Ee)}))),n.addDisplayType((()=>{const a=function(t){const n=t.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=n.exports;return e.ConfigurationSchema("LinearApolloDisplay",{height:{type:"number",defaultValue:500}},{baseConfiguration:a,explicitlyTyped:!0})}(n);return new t.DisplayType({name:"LinearApolloDisplay",configSchema:a,stateModel:In(0,a),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:jn})})),n.addDisplayType((()=>{const a=function(t){const n=t.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=n.exports;return e.ConfigurationSchema("SixFrameFeatureDisplay",{renderer:$t,height:{type:"number",defaultValue:120}},{baseConfiguration:a,explicitlyTyped:!0})}(n),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}=Un(),{height:o,selectedFeature:r}=e;let{detailsHeight:s}=e;return r||(s=0),oe.default.createElement("div",{style:{height:e.height}},oe.default.createElement("div",{className:a.shading,style:{height:o-s}},oe.default.createElement(n,{model:e,...t})),oe.default.createElement("div",{className:"testTrackLines"},oe.default.createElement(_n,{model:e})))}))}(n);return new t.DisplayType({name:"SixFrameFeatureDisplay",configSchema:a,stateModel:Kn(n,a),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:o})})),n.addRendererType((()=>new Gt({name:"ApolloSixFrameRenderer",ReactComponent:jt,configSchema:$t,pluginManager:n}))),n.addToExtensionPoint("Core-extendSession",Xn.bind(this,n)),n.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:K.default,onClick:()=>{const t=a.getSession(e),{leftOffset:n,rightOffset:o}=e,r=e.getSelectedRegions(n,o);t.queueDialog((e=>[Vt,{session:t,handleClose:()=>{e()},region:r[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),n.addToExtensionPoint("Core-extendPluggableElement",Yt),Qn||n.addToExtensionPoint("Core-extendWorker",(e=>"on"in e&&e.on?(e.on("apollo",(async t=>{if("object"!=typeof(a=t)||null===a||!("apollo"in a)||!0!==a.apollo)return;var a;const{apollo:o,messageId:r,method:s}=t;switch(s){case"getSequence":{const{region:a}=t,{assemblyName:s}=a,i=n.rootModel?.session?.apolloDataStore;if(!i)break;const l=i.getBackendDriver(s),{seq:c}=await l.getSequence(a);e.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=t,s=n.rootModel?.session?.apolloDataStore;if(!s)break;const i=s.getBackendDriver(a),l=await i.getRegions(a);e.workers[0].postMessage({apollo:o,messageId:r,regions:l});break}}})),e):e))}configure(e){a.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[ut,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[Et,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[Jt,{session:e,handleClose:()=>{t()}}]))}}))}};
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e=require("@apollo-annotation/apollo-common"),t=require("@apollo-annotation/apollo-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("nanoid"),f=require("@mui/icons-material/Link"),m=require("@mui/material"),g=require("@mui/material/InputAdornment"),p=require("@mui/material/LinearProgress"),h=require("bson-objectid"),y=require("react"),b=require("@jbrowse/core/ui"),w=require("@mui/icons-material/Close"),S=require("mobx-react"),v=require("tss-react/mui"),E=require("@jbrowse/core/util/types/mst"),C=require("jsonpath"),x=require("@jbrowse/core/util/io"),F=require("fast-deep-equal/es6"),A=require("idb/with-async-ittr"),D=require("file-saver"),k=require("@mui/material/Checkbox"),N=require("@mui/material/FormControlLabel"),R=require("@mui/icons-material/Delete"),M=require("@mui/x-data-grid"),T=require("@mui/material/utils"),L=require("autosuggest-highlight/match"),I=require("autosuggest-highlight/parse"),P=require("@mui/icons-material/AccountCircle"),q=require("@jbrowse/core/pluggableElementTypes/AdapterType"),_=require("@jbrowse/core/data_adapters/BaseAdapter"),U=require("@jbrowse/core/util/rxjs"),O=require("@jbrowse/core/util/simpleFeature"),B=require("@jbrowse/core/TextSearch/BaseResults"),j=require("@apollo-annotation/apollo-mst"),$=require("@mui/icons-material/Clear"),G=require("@mui/icons-material/UnfoldLess"),W=require("@jbrowse/core/util/tracks"),H=require("@mui/icons-material/ExpandLess"),z=require("@mui/icons-material/ExpandMore"),V=require("@mui/icons-material/Error");function J(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}function X(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 Y=J(o),K=J(s),Z=J(u),Q=J(f),ee=J(g),te=J(p),ne=J(h),ae=J(y),oe=X(y),re=J(w),se=J(C),le=J(F),ie=J(k),ce=J(N),ue=J(R),de=J(L),fe=J(I),me=J(P),ge=J(q),pe=J(O),he=J(B),ye=J($),be=J(G),we=J(H),Se=J(z),ve=J(V);const Ee=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 Ce(e,t,n){const a=Z.default.parseStringSync(t,{parseSequences:!0,parseComments:!0,parseDirectives:!1,parseFeatures:!0});if(0===a.length)throw new Error("No features found in GFF3 file");let o=0,r=n.assemblies.get(e);r||(r=n.addAssembly(e));for(const e of a)if(Array.isArray(e)){const t=Fe(e),n=r.refSeqs.get(t.refSeq)??r.addRefSeq(t.refSeq,t.refSeq);n.features.has(t._id)||n.addFeature(t)}else if("comment"in e)r.addComment(e.comment);else{o++;let t=r.refSeqs.get(e.id);t||(t=r.addRefSeq(e.id,e.id,e.description)),e.description&&!t.description&&t.setDescription(e.description),t.addSequence({start:0,stop:e.sequence.length,sequence:e.sequence})}if(0===o)throw new Error("No embedded FASTA section found in GFF3");const s=await xe(r);return n.addCheckResults(s),r}async function xe(t){const n=[];for(const a of t.refSeqs.values())for(const t of a.features.values())for(const o of e.checkRegistry.getChecks().values()){const e=await o.checkFeature(i.getSnapshot(t),(async(e,t)=>a.getSequence(e,t)));n.push(...e)}return n}function Fe(e){const[t]=e,{attributes:n,child_features:a,end:o,phase:r,score:s,seq_id:l,source:i,start:c,strand:u,type:f}=t;if(!l)throw new Error(`feature does not have seq_id: ${JSON.stringify(t)}`);if(!f)throw new Error(`feature does not have type: ${JSON.stringify(t)}`);if(null===c)throw new Error(`feature does not have start: ${JSON.stringify(t)}`);if(null===o)throw new Error(`feature does not have end: ${JSON.stringify(t)}`);const m={_id:d.nanoid(),gffId:"",refSeq:l,type:f,start:c-1,end:o};if(e.length>1&&(m.discontinuousLocations=e.map((e=>{const{end:t,phase:n,start:a}=e;if(null===a||null===t)throw new Error(`feature does not have start and/or end: ${JSON.stringify(e)}`);let o;if(n)switch(n){case"0":o=0;break;case"1":o=1;break;case"2":o=2;break;default:throw new Error(`Unknown phase: "${n}"`)}return{start:a-1,end:t,phase:o}}))),u)if("+"===u)m.strand=1;else{if("-"!==u)throw new Error(`Unknown strand: 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new Error("no feature for drag preview??");if(i!==this)throw new Error("drawDragPreview() called on wrong glyph?");const u=this.isMouseOnFeatureEdge(c,l,e);if(!u)return;const{mousePosition:d}=n.current,f=d.bp,m=r(o[c.regionNumber].assemblyName);let g;if("end"===u){const e=l._id;g=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[e],featureId:e,oldEnd:l.end,newEnd:f,assembly:m})}else{const e=l._id;g=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[e],featureId:e,oldStart:l.start,newStart:f,assembly:m})}if(!a)throw new Error("no change manager");a.submit(g),s()}}const In=i.types.model({heightPreConfig:i.types.maybe(i.types.refinement("displayHeight",i.types.number,(e=>e>=20)))}).volatile((()=>({scrollTop:0}))).views((e=>({get height(){return e.heightPreConfig??n.getConf(e,"height")}}))).actions((e=>({setScrollTop(t){e.scrollTop=t},setHeight:t=>(e.heightPreConfig=Math.max(t,20),e.height),resizeHeight(t){const n=e.height;return this.setHeight(e.height+t)-n}})));function Pn(e,t,n,a){return 1===n?(e+a)%3+1:(t-a)%3*-1-1}const qn=[null,"#FF8080","#80FF80","#8080FF","#8080FF","#80FF80","#FF8080"];function _n(e,t){return t?.palette.bases[e.toUpperCase()].main.toString()??"lightgray"}function Un(e,t,n,a,o){const r=Math.min(n,10);e.fillStyle="#000",e.font=`${r}px`;const s=e.measureText(a).width;e.fillText(a,t+(n-s)/2,o+10)}function On(e,t,n,a,o,s,l,i,c,u){let d=l.slice(i,i+3).toUpperCase();c&&(d=function(e){return[...e].map((e=>r.revcom(e))).reverse().join("")}(d));const f=r.defaultCodonTable[d];f&&(e.beginPath(),e.fillStyle=function(e,t,n){const a={M:"#33ee33","*":"#f44336"};return void 0!==a[e?.toUpperCase()]?a[e?.toUpperCase()]:n<=.1?t:"lightgray"}(f,u,t),e.rect(n,a,o,s),e.fill(),t<=.1&&(e.stroke(),Un(e,n,o,f,a)))}let Bn=null,jn=null;if("document"in window)for(const e of["forward","backward"]){const t=document.createElement("canvas"),n=10;t.width=t.height=n;const a=t.getContext("2d");if(a){const o="rgba(0,0,0,0)",r="rgba(255,255,255,0.25)",s="forward"===e?a.createLinearGradient(0,n,n,0):a.createLinearGradient(0,0,n,n);s.addColorStop(0,o),s.addColorStop(.25,o),s.addColorStop(.25,r),s.addColorStop(.5,r),s.addColorStop(.5,o),s.addColorStop(.75,o),s.addColorStop(.75,r),s.addColorStop(1,r),a.fillStyle=s,a.fillRect(0,0,10,10),"forward"===e?Bn=a.createPattern(t,"repeat"):jn=a.createPattern(t,"repeat")}}let $n=null,Gn=null;if("document"in window)for(const e of["forward","backward"]){const t=document.createElement("canvas"),n=10;t.width=t.height=n;const a=t.getContext("2d");if(a){const o="rgba(0,0,0,0)",r="rgba(255,255,255,0.25)",s="forward"===e?a.createLinearGradient(0,n,n,0):a.createLinearGradient(0,0,n,n);s.addColorStop(0,o),s.addColorStop(.25,o),s.addColorStop(.25,r),s.addColorStop(.5,r),s.addColorStop(.5,o),s.addColorStop(.75,o),s.addColorStop(.75,r),s.addColorStop(1,r),a.fillStyle=s,a.fillRect(0,0,10,10),"forward"===e?$n=a.createPattern(t,"repeat"):Gn=a.createPattern(t,"repeat")}}const Wn=new Ln,Hn=new class extends Tn{featuresForRow(e){const t=[];for(const[,n]of e.children??new Map)for(const[,e]of n.children??new Map)"CDS"===e.type&&t.push({parent:n,cds:e});const n=[];for(const e of t){const t=[];for(const[,n]of e.parent.children??new Map)if("CDS"!==n.type||n._id===e.cds._id)if(n.discontinuousLocations&&n.discontinuousLocations.length>0)for(const a of n.discontinuousLocations)t.push({annotationFeature:n,parent:e.parent,start:a.start,end:a.end,phase:a.phase});else t.push({annotationFeature:n,parent:e.parent});t.push({annotationFeature:e.parent}),n.push(t)}return n}getRowCount(e,t){let n=0;for(const[,t]of e.children??new Map)for(const[,e]of t.children??new Map)"CDS"===e.type&&(n+=1);return n}draw(e,t,n,a,o,r){const{apolloRowHeight:s,lgv:l,session:i,theme:c}=e,{bpPerPx:u}=l,d=s,f=Math.round(.6*d),m=Math.round(.9*d),{_id:g,children:p,min:h,strand:y}=n,{apolloSelectedFeature:b}=i;let w=0;for(const[,e]of p??new Map)if("mRNA"===e.type)for(const[,n]of e.children??new Map){if("CDS"!==n.type)continue;const s=(e.start-h)/u,l=e.length/u,i=r?a-s-l:a+s,f=Math.round((w+.5)*d)+o*d;t.strokeStyle=c?.palette.text.primary??"black",t.beginPath(),t.moveTo(i,f),t.lineTo(i+l,f),t.stroke(),w+=1}w=0;for(const[,e]of p??new Map){if("mRNA"!==e.type)continue;const n=[...e.children??[]].filter((([,e])=>"CDS"===e.type)).length;for(let s=0;s<n;s++){for(const[,n]of e.children??new Map){if("exon"!==n.type)continue;const e=(n.start-h)/u,s=n.length/u,l=r?a-e-s:a+e,i=(o+w)*d+(d-f)/2;if(t.fillStyle=c?.palette.text.primary??"black",t.fillRect(l,i,s,f),s>2&&(t.clearRect(l+1,i+1,s-2,f-2),t.fillStyle=b&&n._id===b._id?"rgb(0,0,0)":"rgb(211,211,211)",t.fillRect(l+1,i+1,s-2,f-2),Bn&&jn&&y)){const e=r?-1:1,[n,a]=y*e==1?[Bn,jn]:[jn,Bn];t.fillStyle=n,t.fillRect(l+1,i+1,s-2,(f-2)/2),t.fillStyle=a,t.fillRect(l+1,i+1+(f-2)/2,s-2,(f-2)/2)}}w+=1}}w=0;for(const[,e]of p??new Map)if("mRNA"===e.type)for(const[,n]of e.children??new Map)if("CDS"===n.type){if(n.discontinuousLocations)for(const e of n.discontinuousLocations){const s=(e.start-h)/u,l=(e.end-e.start)/u,i=r?a-s-l:a+s;t.fillStyle=c?.palette.text.primary??"black";const f=(o+w)*d+(d-m)/2;if(t.fillRect(i,f,l,m),l>2){t.clearRect(i+1,f+1,l-2,m-2);const a=Pn(e.start,e.end,e.strand,e.phase),o=qn.at(a)??"rgb(171,71,188)";if(t.fillStyle=b&&n._id===b._id?"rgb(0,0,0)":o,t.fillRect(i+1,f+1,l-2,m-2),Bn&&jn&&y){const e=r?-1:1,[n,a]=y*e==1?[Bn,jn]:[jn,Bn];t.fillStyle=n,t.fillRect(i+1,f+1,l-2,(m-2)/2),t.fillStyle=a,t.fillRect(i+1,f+(m-2)/2,l-2,(m-2)/2)}}}w+=1}if(b)if(g===b._id){const e=n.length/u,s=r?a-e:a,l=o*d,i=this.getRowCount(n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,0.08)",t.fillRect(s,l,e,i)}else{let e,n,s=0;for(const[,t]of p??new Map)t._id===b?._id&&(e=t,n=s),s++;if(void 0===e||void 0===n)return;const l=this.cdsCount(e);let i=d;l>1&&(i*=l);const f=e.length/u,m=r?a-f:a+(e.start-h)/u,g=(o+n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,08)",t.fillRect(m,g,f,i)}}cdsCount(e){let t=0;for(const[,n]of e?.children??new Map)"CDS"===n.type&&n.discontinuousLocations&&n.discontinuousLocations.length>0&&t++;return t}drawHover(e,t,n,a,o){const{apolloHover:r}=e;if(!r)return;const{feature:s}=r;if(s)if(s.discontinuousLocations&&s.discontinuousLocations.length>0)for(const n of s.discontinuousLocations)this.drawShadeForFeature(e,t,n.start,n.end,n.end-n.start);else this.drawShadeForFeature(e,t,s.start,s.end,s.length,n,a,o)}drawShadeForFeature(e,t,n,a,o,r,s,l){const{apolloHover:i,apolloRowHeight:c,displayedRegions:u,lgv:d,theme:f}=e,{bpPerPx:m,bpToPx:g,offsetPx:p}=d;if(!i)return;const{feature:h,topLevelFeature:y}=i;if(!h||!y)return;let b,w,S,v=0;for(const[,e]of y.children??new Map){e._id===h?._id&&(b=e,S=v);for(const[,t]of e.children??new Map)t._id===h._id&&(w=t,b=e,S=v);v++}const E=this.cdsCount(b);if(E>1&&r&&s){if(void 0===b||void 0===S)return;const e=w?w.length/m:b.length/m,n=l?s-e:s+(w?(w.start-h.min)/m:(b.start-h.min)/m),a=(r+S)*c;t.fillStyle=f?.palette.action.selected??"rgba(0,0,0,04)",t.fillRect(n,a,e,c*E)}else{const{mousePosition:e}=i;if(!e)return;const r=c,{regionNumber:s,y:l}=e,d=Math.floor(l/r),h=u[s],{refName:y,reversed:b}=h,w=(g({refName:y,coord:b?a:n,regionNumber:s})?.offsetPx??0)-p,S=d*r,v=o/m;t.fillStyle=f?.palette.action.focus??"rgba(0,0,0,0.04)",t.fillRect(w,S,v,r)}}drawDragPreview(e,t){const{apolloDragging:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e,{bpPerPx:l,offsetPx:i}=r;if(!n)return;const{discontinuousLocation:c,feature:u,glyph:d,mousePosition:f}=n.start;if(!u)throw new Error("no feature for drag preview??");if(d!==this)throw new Error("drawDragPreview() called on wrong glyph?");const{mousePosition:g}=n.current,p=this.isMouseOnFeatureEdge(f,u,e);if(!p)return;const h=Math.floor(f.y/a),y=o[f.regionNumber];let b;b=c?y.reversed?y.end-c[p]:c[p]-y.start:y.reversed?y.end-u[p]:u[p]-y.start;const w=b/l-i,S=Math.min(g.x,w),v=h*a,E=Math.abs(g.x-w),C=1*a;t.strokeStyle=s?.palette.info.main??"rgb(255,0,0)",t.setLineDash([6]),t.strokeRect(S,v,E,C),t.fillStyle=m.alpha(s?.palette.info.main??"rgb(255,0,0)",.2),t.fillRect(S,v,E,C)}isMouseOnFeatureEdge(e,t,n,a){if(!e)return;const{bp:o,refName:r,regionNumber:s,x:l}=e,{lgv:i}=n,{bpToPx:c,offsetPx:u}=i;let d,f;if(t.discontinuousLocations&&t.discontinuousLocations.length>0){let e;for(const n of t.discontinuousLocations)if(o>=n.start&&o<=n.end){e=n;break}if(!e)return;d=c({refName:r,coord:e.start,regionNumber:s}),f=c({refName:r,coord:e.end,regionNumber:s})}else d=c({refName:r,coord:t.start,regionNumber:s}),f=c({refName:r,coord:t.end,regionNumber:s});if(void 0!==d&&void 0!==f){const e=d.offsetPx-u,n=f.offsetPx-u;if(Math.abs(n-e)<8)return;const o=this.getParentFeature(t,a);if(o){if("gene"===o.type)return;if(t.start<=o.start&&Math.abs(e-l)<4)return;if(t.end>=o.end&&Math.abs(n-l)<4)return}if(Math.abs(e-l)<4)return"start";if(Math.abs(n-l)<4)return"end"}}onMouseMove(e,t){const{feature:n,mousePosition:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);e.apolloDragging?e.setCursor("col-resize"):n&&a&&(this.isMouseOnFeatureEdge(a,n,e,o)?e.setCursor("col-resize"):e.setCursor())}onMouseDown(e,t){const{feature:n,mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);n&&a&&this.isMouseOnFeatureEdge(a,n,e)&&t.stopPropagation()}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}startDrag(e){const{feature:t,mousePosition:n,topLevelFeature:a}=e.apolloDragging?.start??{},{mousePosition:o}=e.apolloDragging?.current??{};return!!(t&&n&&o&&this.isMouseOnFeatureEdge(n,t,e,a))}adjacentExonsOfCdsDL(e,t){let n,a,o,r;if(t){for(const[n,a]of t.entries()){const t=a.cdsDL;if(e.start===t?.start&&e.end===t.end&&e.phase===t.phase){r=n;break}}if(void 0!==r){const{exon:e}=t[r];o=e}void 0!==r&&r>0&&(n=t[r-1].exon),void 0!==r&&r<t.length-1&&(a=t[r+1].exon)}return{prevExon:n,matchingExon:o,nextExon:a}}exonCDSRelation(e,t){const n=[];if(!e)return n;const a=this.getParentFeature(e,t);if(!a?.children)return n;for(const[,t]of a.children)if("exon"===t.type){const a=this.cdsDLForExon(t,e);n.push({exon:t,cdsDL:a?{start:a.start,end:a.end,phase:a.phase}:void 0})}return n}cdsDLForExon(e,t){let n;if(t.discontinuousLocations&&t.discontinuousLocations.length>0)for(const a of t.discontinuousLocations)if(a.start>=e.start&&a.end<=e.end){n=a;break}return n}cdsDlsForExon(e,t){const n=[],a=this.getParentFeature(e,t);if(!a?.children||!t)return n;const o=[];for(const[,e]of a.children)"CDS"===e.type&&o.push(e);for(const t of o)for(const[,o]of a.children)if("exon"===o.type&&o._id===e._id){const e=this.cdsDLForExon(o,t);e&&n.push(e)}return n}adjacentExonsOfExon(e,t){const n=this.getParentFeature(e,t);if(!n||!n.children)return;let a,o,r=0;for(const[,t]of n.children){if(t._id===e._id)break;r++}const s=[...n.children.keys()];if(r>0){const e=n.children.get(s[r-1]);e&&"exon"===e.type&&(a=e)}if(r<s.length-1){const e=n.children.get(s[r+1]);e&&"exon"===e.type&&(o=e)}return{prevExon:a,nextExon:o}}continueDrag(e,t){const{discontinuousLocation:n,feature:a,glyph:o,mousePosition:r,topLevelFeature:s}=e.apolloDragging?.start??{};if(!t||!r)return;const{bp:l}=t;if(!a||!t)return;const i=this.isMouseOnFeatureEdge(r,a,e,s);if("CDS"===a.type&&a.discontinuousLocations&&a.discontinuousLocations.length>0&&n){const e=this.exonCDSRelation(a,s),{matchingExon:t,nextExon:o,prevExon:r}=this.adjacentExonsOfCdsDL(n,e);if(o&&l>=o.start-1)return;if(r&&l<=r.end+1)return;if(!r&&o&&t&&l<t.start)return;if(r&&!o&&t&&l>t.end)return;if(i&&("start"===i&&l>=n.end-1||"end"===i&&l<=n.start+1))return}if("CDS"!==a.type){const e=this.adjacentExonsOfExon(a,s);if(e?.nextExon&&l>=e?.nextExon.start-1)return;if(e?.prevExon&&l<=e?.prevExon.end+1)return;const t=this.cdsDlsForExon(a,s);if(t&&t.length>0){let e;for(const n of t)if(i&&("start"===i&&l>=n.start-1||"end"===i&&l<=n.end+1)){e=!0;break}if(e)return}else if(i&&("start"===i&&l>=a.end-1||"end"===i&&l<=a.start+1))return}e.setDragging({start:{feature:a,topLevelFeature:s,glyph:o,discontinuousLocation:n,mousePosition:r},current:{feature:a,topLevelFeature:s,glyph:o,mousePosition:t}})}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];let o;for(const e of a)void 0!==e.start&&void 0!==e.end&&void 0!==e.phase?t>=e.start&&t<=e.end&&e.parent&&(o=e.annotationFeature):t>=e.annotationFeature.start&&t<=e.annotationFeature.end&&e.parent&&(o=e.annotationFeature);return o||(o=a.at(-1)?.annotationFeature),o}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e.annotationFeature._id===t._id)))return e}async executeDrag(e){const{apolloDragging:t,changeManager:n,displayedRegions:a,getAssemblyId:o,setCursor:r}=e;if(!t)return;const{discontinuousLocation:s,feature:l,glyph:i,mousePosition:c,topLevelFeature:u}=t.start;if(!l)throw new Error("no feature for drag preview??");if(i!==this)throw new Error("drawDragPreview() called on wrong glyph?");const d=this.isMouseOnFeatureEdge(c,l,e);if(!d)return;const{mousePosition:f}=t.current,m=f.bp,g=o(a[c.regionNumber].assemblyName),p=[];if("start"===d)if(void 0!==s?.idx&&l.discontinuousLocations&&l.discontinuousLocations.length>0){this.addDiscontinuousLocStartChange(p,l,m,l.discontinuousLocations[s.idx].start,g,s.idx);const e=this.exonCDSRelation(l,u),t=this.adjacentExonsOfCdsDL(s,e);t&&t.matchingExon&&m<t.matchingExon.start&&this.addStartLocationChange(p,t.matchingExon,m,g)}else this.addStartLocationChange(p,l,m,g);else if(void 0!==s?.idx&&l.discontinuousLocations&&l.discontinuousLocations.length>0){this.addDiscontinuousLocEndChange(p,l,m,l.discontinuousLocations[s.idx].end,g,s.idx);const e=this.exonCDSRelation(l,u),t=this.adjacentExonsOfCdsDL(s,e);t&&t.matchingExon&&m>t.matchingExon.end&&this.addEndLocationChange(p,t.matchingExon,m,g)}else this.addEndLocationChange(p,l,m,g);if(!n)throw new Error("no change manager");for(const e of p)await n.submit(e);r()}addDiscontinuousLocStartChange(e,n,a,o,r,s){e.push(new t.DiscontinuousLocationStartChange({typeName:"DiscontinuousLocationStartChange",changedIds:[n._id],featureId:n._id,newStart:a,oldStart:o,index:s,assembly:r}))}addDiscontinuousLocEndChange(e,n,a,o,r,s){e.push(new t.DiscontinuousLocationEndChange({typeName:"DiscontinuousLocationEndChange",changedIds:[n._id],featureId:n._id,newEnd:a,oldEnd:o,index:s,assembly:r}))}addEndLocationChange(e,n,a,o){const r=n._id;e.push(new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[r],featureId:r,oldEnd:n.end,newEnd:a,assembly:o}))}addStartLocationChange(e,n,a,o){const r=n._id;e.push(new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[r],featureId:r,oldStart:n.start,newStart:a,assembly:o}))}},zn=new class extends Ln{featuresForRow(e){const t=[[e]];if(e.children)for(const[,n]of e.children??new Map)t.push(...this.featuresForRow(n));return t}getRowCount(e){return this.featuresForRow(e).length}draw(e,t,n,a,o,r){for(let s=0;s<this.getRowCount(n);s++)this.drawRow(e,t,n,a,o+s,o,r)}drawRow(e,t,n,a,o,r,s){const l=this.featuresForRow(n)[o-r];for(const r of l)this.drawFeature(e,t,n,r,a,o,s)}drawFeature(e,t,n,a,o,r,s){const{apolloRowHeight:l,lgv:i,session:c}=e,{bpPerPx:u}=i,{apolloSelectedFeature:d}=c,f=(a.start-n.min)/u,m=a.length/u,g=s?o-f-m:o+f,p=r*l,h=this.getRowCount(a),y=this.getIsSelectedFeature(a,d);h>1&&this.drawBox(t,g,p,m,h*l,y?"rgba(130,0,0,0.45)":"rgba(255,0,0,0.25)"),super.draw(e,t,a,g,r,s)}drawHover(e,t){const{apolloHover:n,apolloRowHeight:a,displayedRegions:o,lgv:r}=e;if(!n)return;const{feature:s,mousePosition:l}=n;if(!s||!l)return;const{regionNumber:i,y:c}=l,u=o[i],{refName:d,reversed:f}=u,{bpPerPx:m,bpToPx:g,offsetPx:p}=r,{end:h,length:y,start:b}=s,w=(g({refName:d,coord:f?h:b,regionNumber:i})?.offsetPx??0)-p,S=Math.floor(c/a)*a,v=y/m;t.fillStyle="rgba(0,0,0,0.2)",t.fillRect(w,S,v,a*this.getRowCount(s))}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}continueDrag(e,t){}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];return a?.find((e=>t>=e.start&&t<=e.end))}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e._id===t._id)))return e}},Vn=new class extends Tn{featuresForRow(e){const t=[];for(const[,n]of e.children??new Map){const e=[];for(const[,t]of n.children??new Map)e.push(t);e.push(n),t.push(e)}return t}getRowCount(e){let t=0;for(const[,n]of e.children??new Map)"mRNA"===n.type&&(t+=1);return t}draw(e,t,n,a,o,r){const{apolloRowHeight:s,lgv:l,session:i,theme:c}=e,{bpPerPx:u}=l,d=s,f=Math.round(.6*d),m=Math.round(.9*d),{_id:g,children:p,min:h,strand:y}=n,{apolloSelectedFeature:b}=i;let w=0;for(const[,e]of p??new Map){if("mRNA"!==e.type)continue;const n=(e.start-h)/u,s=e.length/u,l=r?a-n-s:a+n,i=Math.round((w+.5)*d)+o*d;t.strokeStyle=c?.palette.text.primary??"black",t.beginPath(),t.moveTo(l,i),t.lineTo(l+s,i),t.stroke(),w+=1}w=0;for(const[,e]of p??new Map){if("mRNA"!==e.type)continue;const n=[...e.children??[]].filter((([,e])=>"CDS"===e.type)).length;for(let s=0;s<n;s++)for(const[,n]of e.children??new Map){const e="CDS"===n.type,s=n.type.endsWith("UTR");if(!e&&!s)continue;const l=(n.start-h)/u,i=n.length/u,g=r?a-l-i:a+l;t.fillStyle=c?.palette.text.primary??"black";const p=e?m:f,S=(o+w)*d+(d-p)/2;if(t.fillRect(g,S,i,p),i>2){t.clearRect(g+1,S+1,i-2,p-2);let a="rgb(211,211,211)";if(e){const e=Pn(n.start,n.end,n.strand,n.phase);a=qn.at(e)??"rgb(171,71,188)"}if(t.fillStyle=b&&n._id===b._id?"rgb(0,0,0)":a,t.fillRect(g+1,S+1,i-2,p-2),$n&&Gn&&y){const e=r?-1:1,[n,a]=y*e==1?[$n,Gn]:[Gn,$n];t.fillStyle=n,t.fillRect(g+1,S+1,i-2,(p-2)/2),t.fillStyle=a,t.fillRect(g+1,S+1+(p-2)/2,i-2,(p-2)/2)}}}w+=1}if(b)if(g===b._id){const e=n.length/u,s=r?a-e:a,l=o*d,i=this.getRowCount(n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,0.08)",t.fillRect(s,l,e,i)}else{let e,n,s=0;for(const[,t]of p??new Map)t._id===b?._id&&(e=t,n=s),s++;if(void 0===e||void 0===n)return;const l=e.length/u,i=r?a-l:a+(e.start-h)/u,f=(o+n)*d;t.fillStyle=c?.palette.action.selected??"rgba(0,0,0,08)",t.fillRect(i,f,l,d)}}drawHover(e,t){const{apolloHover:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e;if(!n)return;const{feature:l,mousePosition:i}=n;if(!l||!i)return;const{regionNumber:c,y:u}=i,{bpPerPx:d,bpToPx:f,offsetPx:m}=r,g=a,p=Math.floor(u/g),h=o[c],{refName:y,reversed:b}=h,w=(f({refName:y,coord:b?l.end:l.start,regionNumber:c})?.offsetPx??0)-m,S=p*g,v=l.length/d;t.fillStyle=s?.palette.action.focus??"rgba(0,0,0,0.04)",t.fillRect(w,S,v,g)}drawDragPreview(e,t){const{apolloDragging:n,apolloRowHeight:a,displayedRegions:o,lgv:r,theme:s}=e,{bpPerPx:l,offsetPx:i}=r;if(!n)return;const{feature:c,glyph:u,mousePosition:d}=n.start;if(!c)throw new Error("no feature for drag preview??");if(u!==this)throw new Error("drawDragPreview() called on wrong glyph?");const{mousePosition:f}=n.current,g=this.isMouseOnFeatureEdge(d,c,e);if(!g)return;const p=Math.floor(d.y/a),h=o[d.regionNumber],y=(h.reversed?h.end-c[g]:c[g]-h.start)/l-i,b=Math.min(f.x,y),w=p*a,S=Math.abs(f.x-y),v=1*a;t.strokeStyle=s?.palette.info.main??"rgb(255,0,0)",t.setLineDash([6]),t.strokeRect(b,w,S,v),t.fillStyle=m.alpha(s?.palette.info.main??"rgb(255,0,0)",.2),t.fillRect(b,w,S,v)}isMouseOnFeatureEdge(e,t,n,a){if(!e)return;const{refName:o,regionNumber:r,x:s}=e,{lgv:l}=n,{bpToPx:i,offsetPx:c}=l,u=i({refName:o,coord:t.start,regionNumber:r}),d=i({refName:o,coord:t.end,regionNumber:r});if(void 0!==u&&void 0!==d){const e=u.offsetPx-c,n=d.offsetPx-c;if(Math.abs(n-e)<8)return;const o=this.getParentFeature(t,a);if(o&&t.start<=o.start&&Math.abs(e-s)<4)return;if(o&&t.end>=o.end&&Math.abs(n-s)<4)return;if(Math.abs(e-s)<4)return"start";if(Math.abs(n-s)<4)return"end"}}onMouseMove(e,t){const{feature:n,mousePosition:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);e.apolloDragging?e.setCursor("col-resize"):n&&a&&(this.isMouseOnFeatureEdge(a,n,e,o)?e.setCursor("col-resize"):e.setCursor())}onMouseDown(e,t){const{feature:n,mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);n&&a&&this.isMouseOnFeatureEdge(a,n,e)&&t.stopPropagation()}onMouseUp(e,t){if(e.apolloDragging??0!==t.button)return;const{feature:n}=e.getFeatureAndGlyphUnderMouse(t);n&&e.setSelectedFeature(n)}startDrag(e){const{feature:t,mousePosition:n,topLevelFeature:a}=e.apolloDragging?.start??{},{mousePosition:o}=e.apolloDragging?.current??{};return!!(t&&n&&o&&this.isMouseOnFeatureEdge(n,t,e,a))}continueDrag(e,t){const{feature:n,glyph:a,mousePosition:o,topLevelFeature:r}=e.apolloDragging?.start??{};if(!t||!o)return;const s=this.getParentFeature(n,r),l=this.getAdjacentFeatures(n,s);if(!n||!t)return;const{bp:i}=t,c=this.isMouseOnFeatureEdge(o,n,e,r);if(!c||!("start"===c&&i>=n.end-1||"end"===c&&i<=n.start+1)){if("CDS"!==n.type){if(l.prevFeature&&!l.nextFeature){if("CDS"===l.prevFeature.type&&i<=l.prevFeature.start+1)return;if("CDS"!==l.prevFeature.type&&i<=l.prevFeature.end+1)return}if(!l.prevFeature&&l.nextFeature){if("CDS"===l.nextFeature.type&&i>=l.nextFeature.end-1)return;if("CDS"!==l.nextFeature.type&&i>=l.nextFeature.start-1)return}}if(l.prevFeature&&l.nextFeature)if("CDS"===n.type){if("CDS"!==l.nextFeature.type&&i>=l.nextFeature.end-1)return;if("CDS"===l.nextFeature.type&&i>=l.nextFeature.start-1)return;if("CDS"!==l.prevFeature.type&&i<=l.prevFeature.start+1)return;if("CDS"===l.prevFeature.type&&i<=l.prevFeature.end+1)return}else{if("CDS"===l.prevFeature.type&&i<=l.prevFeature.start+1)return;if("CDS"!==l.prevFeature.type&&i<=l.prevFeature.end+1)return;if("CDS"!==l.nextFeature.type&&i>=l.nextFeature.start-1)return;if("CDS"===l.nextFeature.type&&i>=l.nextFeature.end-1)return}e.setDragging({start:{feature:n,topLevelFeature:r,glyph:a,mousePosition:o},current:{feature:n,topLevelFeature:r,glyph:a,mousePosition:t}})}}getFeatureFromLayout(e,t,n){const a=this.featuresForRow(e)[n];return a?.find((e=>t>=e.start&&t<=e.end))}getRowForFeature(e,t){const n=this.featuresForRow(e);for(const[e,a]of n.entries())if(a.some((e=>e._id===t._id)))return e}async executeDrag(e){const{apolloDragging:t,changeManager:n,displayedRegions:a,getAssemblyId:o,setCursor:r}=e;if(!t)return;const{feature:s,glyph:l,mousePosition:i,topLevelFeature:c}=t.start;if(!s)throw new Error("no feature for drag preview??");if(l!==this)throw new Error("drawDragPreview() called on wrong glyph?");const u=this.isMouseOnFeatureEdge(i,s,e);if(!u)return;const{mousePosition:d}=t.current,f=d.bp,m=o(a[i.regionNumber].assemblyName),g=this.getParentFeature(s,c),p=this.getAdjacentFeatures(s,g),h=[];if("end"===u){this.addEndLocation(h,s,f,m);const{nextFeature:e}=p;if(!e)return;("CDS"!==s.type&&"CDS"===e.type||"CDS"===s.type&&"CDS"!==e.type)&&this.addStartLocation(h,e,f+1,m)}else{this.addStartLocation(h,s,f,m);const{prevFeature:e}=p;if(!e)return;("CDS"!==s.type&&"CDS"===e.type||"CDS"===s.type&&"CDS"!==e.type)&&this.addEndLocation(h,e,f-1,m)}if(!n)throw new Error("no change manager");for(const e of h)await n.submit(e);r()}getAdjacentFeatures(e,t){let n,a,o=0;if(!e||!t||!t.children)return{prevFeature:n,nextFeature:a};for(const[,n]of t.children){if(n._id===e._id)break;o++}const r=[...t.children.keys()];return o>0&&(n=t.children.get(r[o-1])),o<r.length-1&&(a=t.children.get(r[o+1])),{prevFeature:n,nextFeature:a}}addEndLocation(e=[],n,a,o){const r=n._id;e.push(new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[r],featureId:r,oldEnd:n.end,newEnd:a,assembly:o}))}addStartLocation(e=[],n,a,o){const r=n._id;e.push(new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[r],featureId:r,oldStart:n.start,newStart:a,assembly:o}))}};function Jn(e,t){if("gene"===e.type){let t=!1;for(const[,n]of e.children??new Map)if("mRNA"===n.type)for(const[,e]of n.children??new Map)"exon"===e.type&&(t=!0);return t?Hn:Vn}return e.children?.size?zn:Wn}function Xn(e,t){return"CDS"===e.type&&void 0!==e.phase?-1===e.strand?(e.end-e.phase)%3+(t<=1?5:3):Math.abs((e.start+e.phase)%3-2):t<=1?-1===e.strand?4:3:void 0}function Yn(e,t,n,a,o,r){void 0!==o&&(e.fillStyle=t?.palette.action.focus??"rgba(0,0,0,0.04)",e.fillRect(n,a*o,r,a))}function Kn(e,t){return function(e,t){const o=function(e,t){return function(e,t){const o=function(e,t){return function(e,t){const o=function(e,t){return function(e,t){const o=function(e,t){return i.types.compose(a.BaseDisplay,In).named("BaseLinearApolloDisplay").props({type:i.types.literal("LinearApolloDisplay"),configuration:n.ConfigurationReference(t)}).volatile((e=>({lgv:r.getContainingView(e)}))).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...W.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get session(){return r.getSession(e)},get regions(){return e.lgv.dynamicBlocks.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:Math.round(a),end:Math.round(t)})))},get displayedRegions(){return e.lgv.displayedRegions},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>=200)return"Zoom in to see annotations"}}))).views((e=>({get apolloInternetAccount(){const[t]=e.regions,{internetAccounts:a}=i.getRoot(e),{assemblyName:o}=t,{assemblyManager:r}=e.session,s=r.get(o);if(!s)throw new Error(`No assembly found with name ${o}`);const{internetAccountConfigId:l}=n.getConf(s,["sequence","metadata"]);return a.find((e=>n.getConf(e,"internetAccountId")===l))},get changeManager(){return e.session.apolloDataStore?.changeManager},getAssemblyId(t){const{assemblyManager:n}=e.session,a=n.get(t);if(!a)throw new Error(`Could not find assembly named ${t}`);return a.name},get selectedFeature(){return e.session.apolloSelectedFeature}}))).actions((e=>({setSelectedFeature:t=>e.session.apolloSetSelectedFeature(t),afterAttach(){i.addDisposer(e,l.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&(e.session.apolloDataStore.loadFeatures(e.regions),e.session.apolloDataStore.loadRefSeq(e.regions))}),{name:"LinearApolloDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return o.named("LinearApolloDisplayLayouts").props({featuresMinMaxLimit:5e5}).volatile((()=>({seenFeatures:l.observable.map()}))).views((e=>({get featuresMinMax(){const{assemblyManager:t}=e.session;return e.displayedRegions.map((n=>{const a=t.get(n.assemblyName);let o,s;const{end:l,refName:i,start:c}=n;for(const[,t]of e.seenFeatures)i!==a?.getCanonicalRefName(t.refSeq)||!r.doesIntersect2(c,l,t.min,t.max)||t.length>e.featuresMinMaxLimit||(void 0===o&&({min:o}=t),void 0===s&&({max:s}=t),t.min<o&&({min:o}=t),t.end>s&&({max:s}=t));if(void 0!==o&&void 0!==s)return[o,s]}))}}))).actions((e=>({addSeenFeature(t){e.seenFeatures.set(t._id,t)},deleteSeenFeature(t){e.seenFeatures.delete(t)}}))).views((e=>({get featureLayouts(){const{assemblyManager:t}=e.session;return e.displayedRegions.map(((n,a)=>{const o=t.get(n.assemblyName),s=new Map,l=e.featuresMinMax[a];if(!l)return s;const[c,u]=l,d=[],{end:f,refName:m,start:g}=n;for(const[t,n]of e.seenFeatures.entries()){if(!i.isAlive(n)){e.deleteSeenFeature(t);continue}if(m!==o?.getCanonicalRefName(n.refSeq)||!r.doesIntersect2(g,f,n.min,n.max))continue;const a=Jn(n).getRowCount(n,e.lgv.bpPerPx);let l=0,p=!1;for(;!p;){let e=d.slice(l,l+a);if(e.length<a){for(let t=0;t<a-e.length;t++){const e=d.length;d[e]=Array.from({length:u-c}),s.set(e,[])}e=d.slice(l,l+a)}if(e.map((e=>{const t=n.max-n.min==0?n.min+1:n.max;let a=n.min-c,o=t-c;return n.min-c<0&&(a=0,o=t-n.min),e.slice(a,o).some(Boolean)})).some(Boolean))l+=1;else{for(let e=l;e<l+a;e++){let t=n.min-c,a=n.max-c;n.min-c<0&&(t=0,a=n.max-n.min),d[e].fill(!0,t,a);const o=s.get(e);o?.push([e-l,n])}p=!0}}}return s}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const n of t)for(const[t,a]of n)for(const[n,o]of a)if(0===n){if(e._id===o._id)return{layoutRow:t,featureRow:n};if(o.hasDescendant(e._id)){const n=Jn(o).getRowForFeature(o,e);if(void 0!==n)return{layoutRow:t,featureRow:n}}}}}))).views((e=>({get highestRow(){return Math.max(0,...e.featureLayouts.map((e=>Math.max(...e.keys()))))}}))).actions((e=>({afterAttach(){i.addDisposer(e,l.autorun((()=>{if(e.lgv.initialized&&!e.regionCannotBeRendered())for(const t of e.regions){const n=e.session.apolloDataStore.assemblies.get(t.assemblyName),a=n?.getByRefName(t.refName);for(const[,n]of a?.features??new Map)r.doesIntersect2(t.start,t.end,n.start,n.end)&&!e.seenFeatures.has(n._id)&&e.addSeenFeature(n)}}),{name:"LinearApolloDisplaySetSeenFeatures",delay:1e3}))}})))}(0,t).named("LinearApolloDisplayRendering").props({sequenceRowHeight:15,apolloRowHeight:20,detailsMinHeight:200,detailsHeight:200,lastRowTooltipBufferHeight:40,isShown:!0}).volatile((()=>({canvas:null,overlayCanvas:null,collaboratorCanvas:null,seqTrackCanvas:null,seqTrackOverlayCanvas:null,theme:void 0}))).views((e=>({get featuresHeight(){return(e.highestRow+1)*e.apolloRowHeight+e.lastRowTooltipBufferHeight}}))).actions((e=>({toggleShown(){e.isShown=!e.isShown},setDetailsHeight(t){e.detailsHeight=e.isShown?Math.max(Math.min(t,e.height-100),Math.min(e.height,e.detailsMinHeight)):t},setCanvas(t){e.canvas=t},setOverlayCanvas(t){e.overlayCanvas=t},setCollaboratorCanvas(t){e.collaboratorCanvas=t},setSeqTrackCanvas(t){e.seqTrackCanvas=t},setSeqTrackOverlayCanvas(t){e.seqTrackOverlayCanvas=t},setTheme(t){e.theme=t},afterAttach(){i.addDisposer(e,l.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.collaboratorCanvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);for(const n of e.session.collaborators){const{locations:a}=n;if(0===a.length)continue;let o=0;for(const r of e.lgv.displayedRegions){for(const s of a){if(s.refSeq!==r.refName)continue;const{end:a,refSeq:l,start:i}=s,c=e.lgv.bpToPx({refName:l,coord:i,regionNumber:o});if(!c)continue;const u=c.offsetPx-e.lgv.offsetPx,d=(a-i)/e.lgv.bpPerPx;t.fillStyle="rgba(0,255,0,.2)",t.fillRect(u,1,d,100),t.fillStyle="black",t.fillText(n.name,u+1,11,d-2)}o++}}}}),{name:"LinearApolloDisplayRenderCollaborators"}))}})))}(0,t);return o.actions((e=>({afterAttach(){i.addDisposer(e,l.autorun((async()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;if(e.lgv.bpPerPx>3)return;const t=e.seqTrackCanvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);for(const[n,a]of e.regions.entries()){const o=e.session.apolloDataStore.getBackendDriver(a.assemblyName);if(!o)throw new Error("Failed to get the backend driver");const{seq:s}=await o.getSequence(a);if(!s)return;for(const[o,l]of[...s].entries()){const i=(e.lgv.bpToPx({refName:a.refName,coord:a.start+o,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,c=3/e.lgv.bpPerPx,u=e.displayedRegions[n].reversed?i-c:i;for(let n=2;n>=0;n--){const r=qn.at(n+1)??"#ffffff";(a.start+o)%3===n&&On(t,e.lgv.bpPerPx,u,e.sequenceRowHeight*(2-n),c,e.sequenceRowHeight,s,o,!1,r)}if(e.lgv.bpPerPx<=1){const s=(e.lgv.bpToPx({refName:a.refName,coord:a.start+o,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,i=1/e.lgv.bpPerPx,c=e.displayedRegions[n].reversed?s-i:s;t.beginPath(),t.fillStyle=_n(l,e.theme),t.rect(c,3*e.sequenceRowHeight,i,e.sequenceRowHeight),t.fill(),e.lgv.bpPerPx<=.1&&(t.stroke(),Un(t,c,i,l,3*e.sequenceRowHeight));const u=r.revcom(l);t.beginPath(),t.fillStyle=_n(u,e.theme),t.rect(c,4*e.sequenceRowHeight,i,e.sequenceRowHeight),t.fill(),e.lgv.bpPerPx<=.1&&(t.stroke(),Un(t,c,i,u,4*e.sequenceRowHeight))}for(let n=0;n<=2;n++){const r=qn.at(-(n+1))??"#ffffff";(a.start+o)%3===n&&On(t,e.lgv.bpPerPx,u,e.sequenceRowHeight*((e.lgv.bpPerPx<=1?5:3)+n),c,e.sequenceRowHeight,s,o,!0,r)}}}}}),{name:"LinearApolloDisplayRenderSequence"}))}})))}(0,t).actions((e=>({afterAttach(){i.addDisposer(e,l.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.canvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);for(const[n,a]of e.featureLayouts.entries()){const o=e.displayedRegions[n];for(const[s,l]of a.entries())for(const[a,i]of l){if(a>0)continue;if(!r.doesIntersect2(o.start,o.end,i.min,i.max))continue;const l=(e.lgv.bpToPx({refName:o.refName,coord:i.min,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx;Jn(i).draw(e,t,i,l,s,o.reversed)}}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,t);return o.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0,apolloHover:null}))).views((e=>({getFeatureAndGlyphUnderMouse(t){const n=function(e,t){const n=e.currentTarget,{clientX:a,clientY:o}=e,{left:r,top:s}=n.getBoundingClientRect()||{left:0,top:0},l=a-r,i=o-s,{coord:c,index:u,refName:d}=t.pxToBp(l);return{x:l,y:i,refName:d,bp:c,regionNumber:u}}(t,e.lgv),{bp:a,regionNumber:o,y:r}=n,s=Math.floor(r/e.apolloRowHeight),l=e.featureLayouts[o].get(s);if(!l)return{mousePosition:n};const i=l.find((e=>a>=e[1].min&&a<=e[1].max));if(!i)return{mousePosition:n};const[c,u]=i,d=Jn(u);return{feature:d.getFeatureFromLayout(u,a,c),topLevelFeature:u,glyph:d,mousePosition:n}}}))).actions((e=>({continueDrag(t){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");t.stopPropagation();const{glyph:n}=e.apolloDragging.start,{mousePosition:a}=e.getFeatureAndGlyphUnderMouse(t);a&&n&&n.continueDrag(e,a)},setDragging(t){e.apolloDragging=t??null}}))).actions((e=>({setApolloHover(t){e.apolloHover=t},setCursor(t){e.cursor!==t&&(e.cursor=t)}}))).actions((()=>({onClick(){}})))}(0,t).actions((e=>({afterAttach(){i.addDisposer(e,l.autorun((async()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.seqTrackOverlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);const{apolloHover:n,displayedRegions:a,lgv:o,regions:r,sequenceRowHeight:s,theme:l}=e;if(!n)return;const{feature:i,mousePosition:c}=n;if(i&&c)for(const[e,n]of r.entries()){const r=Xn(i,o.bpPerPx);if(i.discontinuousLocations&&i.discontinuousLocations.length>0)for(const c of i.discontinuousLocations){const i=(o.bpToPx({refName:n.refName,coord:c.start,regionNumber:e})?.offsetPx??0)-o.offsetPx,u=(c.end-c.start)/o.bpPerPx;Yn(t,l,a[e].reversed?i-u:i,s,r,u)}else{const c=(o.bpToPx({refName:n.refName,coord:i.start,regionNumber:e})?.offsetPx??0)-o.offsetPx,u=i.length/o.bpPerPx;Yn(t,l,a[e].reversed?c-u:c,s,r,u)}}}),{name:"LinearApolloDisplayRenderSeqHighlight"}))}})))}(0,t);return o.views((e=>({contextMenuItems(t){const{apolloHover:n}=e,{topLevelFeature:a}=n??{};return a&&t?Jn(a).getContextMenuItems(e):[]}}))).actions((e=>({startDrag(t){const{feature:n,glyph:a,mousePosition:o,topLevelFeature:r}=e.getFeatureAndGlyphUnderMouse(t);if(n&&r&&a&&o){let s,l;if(n.discontinuousLocations&&n.discontinuousLocations.length>0)for(let e=0;e<n.discontinuousLocations.length;e++)if(o.bp>=n.discontinuousLocations[e].start&&o.bp<=n.discontinuousLocations[e].end){l=e,s=n.discontinuousLocations[l];break}e.apolloDragging={start:{glyph:a,feature:n,topLevelFeature:r,discontinuousLocation:s?{start:s.start,end:s.end,phase:s.phase,idx:l}:void 0,mousePosition:o},current:{glyph:a,feature:n,topLevelFeature:r,mousePosition:o}},a.startDrag(e,t)||(e.apolloDragging=null)}},endDrag(t){e.continueDrag(t),e.apolloDragging?.start.glyph?.executeDrag(e,t),e.setDragging()}}))).actions((e=>({onMouseDown(t){const{feature:n,glyph:a,topLevelFeature:o}=e.getFeatureAndGlyphUnderMouse(t);a&&n&&o&&a.onMouseDown(e,t)},onMouseMove(t){const{buttons:n}=t,a=e.getFeatureAndGlyphUnderMouse(t),{glyph:o}=a;if(o&&o.onMouseMove(e,t),n)1===n&&(e.apolloDragging?e.continueDrag(t):e.startDrag(t));else{const{feature:t,topLevelFeature:n}=a;t&&o&&n?e.setApolloHover(a):(e.setApolloHover(null),e.setCursor())}},onMouseLeave(t){e.setDragging();const{glyph:n}=e.getFeatureAndGlyphUnderMouse(t);n&&n.onMouseLeave(e,t)},onMouseUp(t){const{glyph:n}=e.getFeatureAndGlyphUnderMouse(t);n&&n.onMouseUp(e,t),e.apolloDragging&&e.endDrag(t)}}))).actions((e=>({afterAttach(){i.addDisposer(e,l.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.overlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);const{apolloDragging:n,apolloHover:a,displayedRegions:o,featureLayouts:r,lgv:s}=e;if(!a)return;const{feature:l,glyph:i}=a;if(!l)return;let c=0,u=0,d=!1;for(const[e,t]of r.entries()){const n=o[e];for(const[a,o]of t.entries())if(0===c)for(const[,t]of o)for(const[,o]of t.children??new Map)if(0===c)if(u=(s.bpToPx({refName:n.refName,coord:l.min,regionNumber:e})?.offsetPx??0)-s.offsetPx,({reversed:d}=n),o._id!==l._id)for(const[,e]of o.children??new Map)0===c&&(e._id!==l._id||(c=a));else c=a}i?.drawHover(e,t,c,u,d),i?.drawTooltip(e,t),n&&n.start.glyph?.drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,t).props({tabularEditor:i.types.optional(Mn,{})}).named("LinearApolloDisplay")}const Zn=v.makeStyles()((e=>({canvasContainer:{position:"relative",left:0},canvas:{position:"absolute",left:0},ellipses:{textOverflow:"ellipsis",overflow:"hidden"},avatar:{position:"absolute",color:e.palette.warning.light,backgroundColor:e.palette.warning.contrastText}}))),Qn=S.observer((function(e){const t=m.useTheme(),{model:n}=e,{apolloRowHeight:a,contextMenuItems:o,cursor:s,featuresHeight:l,isShown:i,onMouseDown:c,onMouseLeave:u,onMouseMove:d,onMouseUp:f,regionCannotBeRendered:g,session:p,setCanvas:h,setCollaboratorCanvas:w,setOverlayCanvas:S,setSeqTrackCanvas:v,setSeqTrackOverlayCanvas:E,setTheme:C,tabularEditor:x}=n,{classes:F}=Zn(),A=r.getContainingView(n);y.useEffect((()=>C(t)),[t,C]);const[D,k]=y.useState(),[N,R]=y.useState([]),M=g();if(!i)return null;const{assemblyManager:T}=p;return ae.default.createElement(ae.default.Fragment,null,A.bpPerPx<=3?ae.default.createElement("div",{className:F.canvasContainer,style:{width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95}},ae.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),v(e)},width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95,className:F.canvas,"data-testid":"seqTrackCanvas"}),ae.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),E(e)},width:A.dynamicBlocks.totalWidthPx,height:A.bpPerPx<=1?125:95,className:F.canvas,"data-testid":"seqTrackOverlayCanvas"})):null,ae.default.createElement("div",{className:F.canvasContainer,style:{width:A.dynamicBlocks.totalWidthPx,height:l},onContextMenu:e=>{if(e.preventDefault(),N.length>0)R([]);else{const t=[e.clientX,e.clientY];k(t),R(o(t))}}},M?ae.default.createElement(m.Alert,{severity:"warning",classes:{message:F.ellipses}},ae.default.createElement(m.Tooltip,{title:M},ae.default.createElement("div",null,M))):ae.default.createElement(ae.default.Fragment,null,ae.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),w(e)},width:A.dynamicBlocks.totalWidthPx,height:l,className:F.canvas,"data-testid":"collaboratorCanvas"}),ae.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),h(e)},width:A.dynamicBlocks.totalWidthPx,height:l,className:F.canvas,"data-testid":"canvas"}),ae.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),S(e)},width:A.dynamicBlocks.totalWidthPx,height:l,onMouseMove:d,onMouseLeave:u,onMouseDown:c,onMouseUp:f,onClick:()=>{x.showPane()},className:F.canvas,style:{cursor:s??"default"},"data-testid":"overlayCanvas"}),A.displayedRegions.flatMap(((e,t)=>{const o=T.get(e.assemblyName);return[...p.apolloDataStore.checkResults.values()].filter((t=>o?.isValidRefName(t.refSeq)&&o?.getCanonicalRefName(t.refSeq)===e.refName&&r.doesIntersect2(e.start,e.end,t.start,t.end))).map((o=>{const r=(A.bpToPx({refName:e.refName,coord:o.start,regionNumber:t})?.offsetPx??0)-A.offsetPx,[s]=o.ids;if(!s)return null;const{topLevelFeature:l}=s,i=parent?n.getFeatureLayoutPosition(l)?.layoutRow??0:0;return ae.default.createElement(m.Tooltip,{key:o._id,title:o.message},ae.default.createElement(m.Avatar,{className:F.avatar,style:{top:i*a,left:r,height:a,width:a}},ae.default.createElement(ve.default,null)))}))})),ae.default.createElement(b.Menu,{open:N.length>0,onMenuItemClick:(e,t)=>{t(),R([])},onClose:()=>{R([])},TransitionProps:{onExit:()=>{R([])}},anchorReference:"anchorPosition",anchorPosition:D?{top:D[1],left:D[0]}:void 0,style:{zIndex:t.zIndex.tooltip},menuItems:N}))))})),ea=S.observer((function({model:e}){const{height:t}=e;return ae.default.createElement("div",{style:{position:"absolute",left:0,top:t/2,width:"100%"}},ae.default.createElement("hr",{style:{margin:0,top:0,color:"black"}}))})),ta=v.makeStyles()((e=>({shading:{background:m.alpha(e.palette.primary.main,.2),overflowY:"scroll",overflowX:"hidden"},details:{background:e.palette.background.paper},accordionControl:{height:12,width:"100%","&:hover":{background:e.palette.action.hover},display:"flex",alignItems:"center",justifyContent:"center"},accordionRoot:{background:e.palette.divider},resizeHandle:{width:"100%",height:4,position:"absolute",cursor:"row-resize",zIndex:100},expandIcon:{},title:{userSelect:"none"}}))),na=({onResize:e})=>{const{classes:t}=ta(),n=y.useCallback((t=>{t.stopPropagation(),t.preventDefault(),e(t.movementY)}),[e]),a=y.useCallback((e=>{e.stopPropagation(),e.preventDefault(),window.removeEventListener("mousemove",n),window.removeEventListener("mouseup",a),window.removeEventListener("mouseleave",a)}),[n]);return ae.default.createElement("div",{onMouseDown:e=>{e.stopPropagation(),window.addEventListener("mousemove",n),window.addEventListener("mouseup",a),window.addEventListener("mouseleave",a)},onClick:e=>{e.stopPropagation(),e.preventDefault()},className:t.resizeHandle})},aa=S.observer((function({onClick:e,onResize:t,open:n,title:a}){const{classes:o}=ta();return ae.default.createElement("div",{className:o.accordionRoot},n&&t?ae.default.createElement(na,{onResize:t}):null,ae.default.createElement("div",{className:o.accordionControl,onClick:e},ae.default.createElement(n?we.default:Se.default,{className:o.expandIcon}),a?ae.default.createElement(m.Typography,{className:o.title,variant:"caption",component:"span"},a):null))})),oa=S.observer((function({model:e,...t}){const{classes:n}=ta(),{height:a,isShown:o,selectedFeature:r,tabularEditor:s,toggleShown:l}=e,i=s.isShown?e.detailsHeight:0,c=o?a-i-24:0,u=y.useRef(null);return y.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,u)),[e,r]),ae.default.createElement("div",{className:n.details,style:{height:a}},ae.default.createElement(aa,{open:o,title:"Graphical",onClick:l}),ae.default.createElement("div",{className:n.shading,ref:u,style:{height:c}},ae.default.createElement(Qn,{model:e,...t})),ae.default.createElement(aa,{title:"Table",open:s.isShown,onClick:s.togglePane,onResize:t=>{e.setDetailsHeight(e.detailsHeight-t)}}),ae.default.createElement("div",{style:{height:i}},ae.default.createElement(Rn,{model:e})))})),ra=i.types.model("JobsManager",{}).views((e=>({get jobStatusWidget(){const{widgets:t}=r.getSession(e);let n=t.get("JobsList");return 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 sa{clientStore;constructor(e){this.clientStore=e}}class la{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 sa{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 Ae(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 Ae(h,"getFeatures failed");throw new Error(e)}return await this.checkSocket(t,o,d),h.json()}async checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),s=`${t}-${n}`,l=new la(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),w=new URLSearchParams({refSeq:f,start:String(i),end:String(s)});b.search=w.toString();const S=b.toString(),v=this.getSeqFromServer(h,S,g,i,s);this.inFlight.set(t,v);const E=await v;return await this.checkSocket(o,l,h),this.inFlight.delete(t),{seq:E,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 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 Ae(l,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return l.ok||(i.ok=!1),i}}class ca extends sa{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 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 ua extends sa{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 Ce(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 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 xe(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 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.makeGFF3Feature(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=Z.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(l,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function da(e,t){const a=new AbortController,{signal:o}=a,s=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",j.AnnotationFeature),c=function(e){const t=i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map(j.ApolloAssembly),checkResults:i.types.map(j.CheckResult)}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly:t=>e.assemblies.put({_id:t,refSeqs:{}}),addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${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,j.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 la(e),collaborationServerDriver:new ia(e),inMemoryFileDriver:new ca(e),desktopFileDriver:r.isElectron?new ua(e):void 0,ontologyManager:Ke.create()}))).actions((e=>({afterCreate(){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 ${a}`);return l}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:s}=n;let l=e.assemblies.get(r);l||(l=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=l.refSeqs.get(i.refSeq);c||(c=l.refSeqs.put({_id:i.refSeq,name:s,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:s,refName:l,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:l,sequence:[]})),u.addSequence({start:i,stop:s,sequence:o})}}))})));return i.types.snapshotProcessor(t,{postProcessor:e=>(e.assemblies={},e.checkResults={},e)})}(s);return t.props({apolloDataStore:i.types.optional(c,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(s),jobsManager:i.types.optional(ra,{})}).extend((()=>{const e=l.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,a){const o=`apollo_track_${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 e=t;if(e.initialized){const{dynamicBlocks:t}=e;t.forEach((e=>{if(void 0!==e.regionNumber){const{assemblyName:t,end:a,refName:o,start:r}=e;n.push({assemblyName:t,refName:o,start:r,end:a})}}))}}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{internetAccounts:t}=i.getRoot(e);l.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const e=t;if(e.initialized){const{dynamicBlocks:t}=e;t.forEach((e=>{if(void 0!==e.regionNumber){const{assemblyName:t,end:a,refName:o,start:r}=e;n.push({assemblyName:t,refName:o,start:r,end:a})}}))}}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)}}),{name:"ApolloSession"});for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t,configuration:a}=n,r=new URL("assemblies",t).href,s=n.getFetcher({locationType:"UriLocation",uri:r});let l,i;try{l=yield s(r,{signal:o})}catch(e){console.error(e);continue}if(l.ok){try{i=yield l.json()}catch(e){console.error(e);continue}for(const r of i){const{addAssembly:s,addSessionAssembly:l,assemblyManager:i}=e,c=i.get(r.name);if(c){e.addApolloTrackConfig(c,t);continue}const u=new URL("refSeqs",t),d=new URLSearchParams({assembly:r._id});u.search=d.toString();const f=u.toString(),m=n.getFetcher({locationType:"UriLocation",uri:f}),g=yield m(f,{signal:o});if(!g.ok){let e;try{e=yield g.text()}catch{e=""}throw new Error(`Failed to fetch fasta info — ${g.status} (${g.statusText})${e?` (${e})`:""}`)}const p=yield g.json(),h={},y=p.map((e=>(h[e.name]=e._id,{refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`}))),b={name:r._id,aliases:[r.name,...r.aliases??[]],displayName:r.displayName??r.name,sequence:{trackId:`sequenceConfigId-${r.name}`,type:"ReferenceSequenceTrack",adapter:{type:"ApolloSequenceAdapter",assemblyId:r._id,baseURL:{uri:t,locationType:"UriLocation"}},metadata:{apollo:!0,internetAccountConfigId:a.internetAccountId,ids:h}},refNameAliases:{adapter:{type:"FromConfigAdapter",features:y}}};(l||s)(b);const w=yield i.waitForAssembly(b.name);e.addApolloTrackConfig(w,t)}}else{const e=yield Ae(l,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){a.abort()}})))}const fa={0:2,1:1,2:0},ma={3:0,4:1,5:2};function ga(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(),...W.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(){const t=r.getSession(e);return t.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.end>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 ma;let i,c,u;l?(i=(t.length+n)%3,c=(ma[a]+i+3)%3,u=r.reverse(t).slice(c)):(i=3-n%3,c=(fa[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()}]})))}const pa="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const ha=new t.CDSCheck;e.checkRegistry.registerCheck(ha.name,ha),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends Y.default{name="ApolloPlugin";version="0.1.1";configurationSchema=Xt;install(e){!function(e){e.addAdapterType((()=>new ge.default({name:"ApolloSequenceAdapter",configSchema:Ot,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Ut})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:zt,AdapterClass:Wt,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:fn,ReactComponent:dn})})),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:Ee,stateModel:Pt(Ee)}))),e.addDisplayType((()=>{const t=function(e){const t=e.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=t.exports;return n.ConfigurationSchema("LinearApolloDisplay",{height:{type:"number",defaultValue:500}},{baseConfiguration:a,explicitlyTyped:!0})}(e);return new a.DisplayType({name:"LinearApolloDisplay",configSchema:t,stateModel:Kn(0,t),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:oa})})),e.addDisplayType((()=>{const t=function(e){const t=e.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=t.exports;return n.ConfigurationSchema("SixFrameFeatureDisplay",{renderer:$t,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),ae.default.createElement("div",{style:{height:e.height}},ae.default.createElement("div",{className:a.shading,style:{height:o-s}},ae.default.createElement(n,{model:e,...t})),ae.default.createElement("div",{className:"testTrackLines"},ae.default.createElement(ea,{model:e})))}))}(e);return new a.DisplayType({name:"SixFrameFeatureDisplay",configSchema:t,stateModel:ga(e,t),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((()=>new Gt({name:"ApolloSixFrameRenderer",ReactComponent:jt,configSchema:$t,pluginManager:e}))),e.addToExtensionPoint("Core-extendSession",da.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:K.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[Vt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Yt),pa||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}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[ut,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Ft,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[Ct,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[Jt,{session:e,handleClose:()=>{t()}}]))}}))}};
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