@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.8

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

@@ -1,2 +1,2 @@
-"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var 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t=a.objectStore("nodes");t.createIndex("by-label","lbl"),t.createIndex("by-type","type"),t.createIndex("by-synonym",["meta","synonyms","val"]),t.createIndex("full-text-words","fullTextWords",{multiEntry:!0})}if(!e.objectStoreNames.contains("edges")){e.createObjectStore("edges",{autoIncrement:!0});const t=a.objectStore("edges");t.createIndex("by-subject","sub"),t.createIndex("by-object","obj"),t.createIndex("by-predicate","pred")}}})}function ct(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function ut(e){const t=Date.now();let n,a=1;this.options.update?.("Parsing JSON",a);try{n=JSON.parse(await A.openLocation(this.sourceLocation).readFile("utf8"))}catch{throw new Error("Error in loading ontology")}a+=5,this.options.update?.("Parsing JSON complete",a);const o=Date.now(),[r,...l]=n.graphs??[];if(r){if(l.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 l=n.objectStore("nodes"),s=dt.call(this).map((e=>e.jsonPath));if(r.nodes){let e=Math.round(a);for(const[,t]of r.nodes.entries())a+=1/r.nodes.length*64,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing nodes",a),e=Math.round(a)),rt(t)&&await l.add({...t,fullTextWords:ct(nt(t,s,this.prefixes))})}const i=n.objectStore("edges");if(r.edges){let e=Math.round(a);for(const[,t]of r.edges.entries())a+=1/r.edges.length*30,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing edges",a),e=Math.round(a)),lt(t)&&await i.add(t)}await n.done;const c=e.transaction("meta","readwrite"),{update:u,...d}=this.options;await c.objectStore("meta").add({ontologyRecord:{name:this.ontologyName,version:this.ontologyVersion,sourceLocation:this.sourceLocation},storeOptions:d,graphMeta:r.meta,timestamp:String(new Date),schemaVersion:2,timings:{overall:Date.now()-t,load:Date.now()-o}},"meta"),await c.done}catch(t){throw await e.transaction("meta","readwrite").objectStore("meta").clear(),t}}}function dt(){return[{displayName:"ID",jsonPath:Ye},...this.options.textIndexing?.indexFields??ht]}async function ft(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&ge.default(this.options.prefixes,t.storeOptions.prefixes)&&ge.default(this.options.textIndexing,t.storeOptions.textIndexing)}class mt{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=ut;getTermsByFulltext=at;openDatabase=it;isDatabaseCurrent=ft;get textIndexFields(){return dt.call(this)}get prefixes(){return this.options.prefixes??new Map}DEFAULT_MAX_SEARCH_RESULTS=100;constructor(e,t,n,a){this.ontologyName=e,this.ontologyVersion=t,this.sourceLocation=n,this.options=a??{},this.db=this.prepareDatabase()}validate(){const e=[],{sourceLocation:t,sourceType:n}=this;return n?"obo-graph-json"!==n&&e.push(new Error(`ontology source file ${JSON.stringify(t)} has type ${n}, which is not yet supported`)):e.push(new Error(`unable to determine format of ontology source file ${JSON.stringify(t)}, file name must end with ".json", ".obo", or ".owl"`)),e}get sourceType(){if(r.isUriLocation(this.sourceLocation)){if(this.sourceLocation.uri.endsWith(".json"))return"obo-graph-json"}else if(r.isLocalPathLocation(this.sourceLocation)&&this.sourceLocation.localPath.endsWith(".json"))return"obo-graph-json"}get dbName(){return`Apollo Ontology "${this.ontologyName}" "${this.ontologyVersion}"`}async prepareDatabase(){const e=this.validate();if(e.length>0)throw e;const t=await this.openDatabase(this.dbName);if(await this.isDatabaseCurrent(t))return t;try{const{options:e,sourceLocation:n,sourceType:a}=this;if("obo-graph-json"!==a)throw new Error(`ontology source file ${JSON.stringify(n)} has type ${a}, which is not yet supported`);return e.update?.("",0),await this.loadOboGraphJson(t),e.update?.("",100),t}catch(e){throw t.close(),await C.deleteDB(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const a of e)t.has(a.id)||(t.set(a.id,!0),n.push(a));return n}async getTermsWithLabelOrSynonym(e,t,n){const a=t?.includeSubclasses??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=r.objectStore("nodes"),s=[...await l.index("by-label").getAll(e),...await l.index("by-synonym").getAll(e)];if(a){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",r);for(const t of e){const e=await l.get(t);e&&s.push(e)}}return s}async getPropertiesByLabel(e,t,n){const a=t?.includeSubProperties??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},r)).filter((e=>St(e)));if(a){const e=await this.recurseEdges("by-object",l.map((e=>e.id)),(e=>"subPropertyOf"===e.pred),"sub",r),t=r.objectStore("nodes");for(const n of e){const e=await t.get(n);e&&St(e)&&l.push(e)}}return l}async 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vt({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:a,ontologyName:o,ontologyVersion:r,renderInput:l,session:s,style:i,value:c}){const[u,d]=y.useState(!1),[f,m]=y.useState(),[g,h]=y.useState(""),[b,S]=y.useState(),{ontologyManager:w}=s.apolloDataStore,v=w.findOntology(o,r)?.dataStore,E=v&&u&&!f,C=v&&!b,T=y.useCallback((e=>(n||!st(e))&&(!t||t(e))),[t,n]);y.useEffect((()=>{u||m(void 0)}),[u]),y.useEffect((()=>{const e=new AbortController,{signal:t}=e;return C&&(h(""),async function(e,t,n,a){if(!t)return;const o=(await e.getTermsWithLabelOrSynonym(t,{includeSubclasses:!1})).find((e=>(n??(()=>!0))(e)));if(!o)throw new Error(`not a valid ${e.ontologyName} term`);return o}(v,c,T).then((e=>{t.aborted||S(e)}),(e=>{t.aborted||x.isAbortException(e)||h(String(e))}))),()=>{e.abort()}}),[s,c,T,v,C]),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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Et({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{notify:l}=a,[s,i]=y.useState(String(r.max)),[c,u]=y.useState(String(r.min+1)),[d,f]=y.useState(""),[m,g]=y.useState(""),[h,b]=y.useState(""),S=Number(s)<=Number(c);return de.default.createElement(We,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},de.default.createElement("form",{onSubmit:async function(a){a.preventDefault(),g("");const i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new ue.default).toHexString(),refSeq:r.refSeq,min:Number(c)-1,max:Number(s),type:d},parentFeatureId:r._id});await e.submit(i),l("Feature added 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v=Boolean(w)||!(i&&l&&u);return u!==Ct.CUSTOM||f||(v=!0),de.default.createElement(We,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},de.default.createElement("form",{onSubmit:async function(s){let c;s.preventDefault(),S("");for(const[,e]of o.apolloDataStore.assemblies??new Map)if(e._id===a.assemblyName)for(const[,t]of e.refSeqs??new Map)t.name===a.refName&&(c=t._id);if(!c)return void S("Invalid refseq id");if(u===Ct.GENE_AND_SUBFEATURES){const o=xt(c,g,Number(i)-1,Number(l)),s={};s[o._id]=o;const u=(new ue.default).toHexString(),d=new t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:u,refSeq:c,min:Number(i)-1,max:Number(l),type:"gene",strand:g,children:s}});return await e.submit(d),r("Feature added successfully","success"),void n()}if(u===Ct.TRANSCRIPT_AND_SUBFEATURES){const o=xt(c,g,Number(i)-1,Number(l)),s=new t.AddFeatureChange({changedIds:[o._id],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:o});return await e.submit(s),r("Feature added successfully","success"),void n()}if(!f)return void S("No type selected");const d=(new ue.default).toHexString(),m=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(i)-1,max:Number(l),type:f,strand:g}});await e.submit(m),r("Feature added successfully","success"),n()},"data-testid":"submit-form"},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(i),onChange:e=>{c(e.target.value)}}),de.default.createElement(p.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:l,onChange:e=>{s(e.target.value)},error:w,helperText:w?'"End" must be greater than 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0}),de.default.createElement(p.MenuItem,{value:1},"+"),de.default.createElement(p.MenuItem,{value:-1},"-"))),de.default.createElement(p.FormControl,{style:{marginTop:20}},de.default.createElement(p.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Ct.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:u,onChange:e=>{S("");const{value:t}=e.target;Object.keys(Ct).includes(t)&&d(Ct[t])}},de.default.createElement(p.FormControlLabel,{value:Ct.GENE_AND_SUBFEATURES,control:de.default.createElement(p.Radio,null),label:de.default.createElement(p.Box,{display:"flex",alignItems:"center"},"Add gene and sub-features",de.default.createElement(p.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and 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Nt({changeManager:e,handleClose:n,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:s,notify:c}=o,u=s.assemblyList,[d,f]=y.useState(u.find((e=>e.name!==r))?.name),[m,g]=y.useState([]),[h,b]=y.useState(""),[S,w]=y.useState(l.min),[v,E]=y.useState("");function C(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=C(a,t);e.refSeq=h,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),o="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:a,children:e.children&&n,_id:o}}return y.useEffect((()=>{b(""),async function(){if(!d)return void E("No assemblies to copy to");const e=await s.waitForAssembly(d);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const n=[...Object.entries(t)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t})));g(n),b(n[0]?._id||"")}().catch((e=>{E(String(e))}))}),[d,s]),de.default.createElement(We,{open:!0,title:"Copy features and 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de.default.createElement(p.TextField,{...n,type:"text",onChange:function(e){o(e.target.value)},value:a,onKeyDown:e=>{"Enter"===e.key?s?.blur():"Escape"===e.key&&(o(String(t)),l(!0))},onBlur:()=>{const n=Number(a);a!==String(t)&&(Number.isNaN(n)?o(String(t)):e(n))},inputRef:e=>{i(e)},error:c,helperText:c?"Not a valid number":void 0})})),Sn=v.observer((function({assembly:e,feature:n,session:a}){const[o,r]=y.useState(""),[l,s]=y.useState(""),{_id:i,assemblyId:c,max:u,min:d,strand:f,type:m}=n,g=e=>{a.notify(e.message,"error")},{changeManager:h}=a.apolloDataStore;function b(n){const{value:a}=n.target,o=a?Number(a):void 0,r=new t.StrandChange({typeName:"StrandChange",changedIds:[i],featureId:i,oldStrand:f,newStrand:o,assembly:e});return h.submit(r)}return de.default.createElement("div",{"data-testid":"basic_information"},de.default.createElement(bn,{margin:"dense",id:"start",label:"Start",fullWidth:!0,variant:"outlined",value:d+1,onChangeCommitted:function(n){n--;const a=new 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n=(e.lgv.bpToPx({refName:o.refName,coord:o.start+l,regionNumber:t})?.offsetPx??0)-e.lgv.offsetPx,i=1/e.lgv.bpPerPx,c=e.lgv.displayedRegions[t].reversed?n-i:n;a.beginPath(),a.fillStyle=Ua(s,e.theme),a.rect(c,3*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),$a(a,c,i,s,3*e.sequenceRowHeight));const u=r.revcom(s);a.beginPath(),a.fillStyle=Ua(u,e.theme),a.rect(c,4*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),$a(a,c,i,u,4*e.sequenceRowHeight))}for(let t=0;t<=2;t++)(o.start+l)%3===t&&ja(a,e.lgv.bpPerPx,u,e.sequenceRowHeight*((e.lgv.bpPerPx<=1?5:3)+t),n,e.sequenceRowHeight,c,l,!0,e.showStartCodons,e.showStopCodons,e.highContrast)}}}),{name:"LinearApolloDisplayRenderSequence"}))}})))}(0,t).actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{const{canvas:t,featureLayouts:n,featuresHeight:a,lgv:o}=e;if(!o.initialized||e.regionCannotBeRendered())return;const{displayedRegions:l,dynamicBlocks:s}=o,i=t?.getContext("2d");if(i){i.clearRect(0,0,s.totalWidthPx,a);for(const[t,a]of n.entries()){const n=l[t];for(const[o,l]of a.entries())for(const[a,s]of l){const l=e.getAnnotationFeatureById(s);a>0||!l||r.doesIntersect2(n.start,n.end,l.min,l.max)&&e.getGlyph(l).draw(i,l,o,e,t)}}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,t);return n.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0,apolloHover:void 0}))).views((e=>({getMousePosition(t){const n=function(e,t){const n=e.currentTarget,{clientX:a,clientY:o}=e,{left:r,top:l}=n.getBoundingClientRect(),s=a-r,i=o-l,{coord:c,index:u,refName:d}=t.pxToBp(s);return{x:s,y:i,refName:d,bp:c,regionNumber:u}}(t,e.lgv),{bp:a,regionNumber:o,y:r}=n,l=Math.floor(r/e.apolloRowHeight),s=e.featureLayouts[o].get(l);if(!s)return n;const i=s.find((t=>{const n=e.getAnnotationFeatureById(t[1]);return n&&a>=n.min&&a<=n.max}));if(!i)return n;const[c,u]=i,d=e.getAnnotationFeatureById(u);if(!d)return n;const f=e.getGlyph(d),{featureTypeOntology:m}=e.session.apolloDataStore.ontologyManager;if(!m)throw new Error("featureTypeOntology is undefined");const g=f.getFeatureFromLayout(d,a,c,m);return g?{...n,featureAndGlyphUnderMouse:{feature:g,topLevelFeature:d,glyph:f}}:n}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");n.stopPropagation(),e.apolloDragging={...e.apolloDragging,current:t}},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,s.autorun((()=>{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,lgv:a,regions:o,sequenceRowHeight:l,session:s,theme:i}=e;if(!n)return;const{feature:c}=n,{featureTypeOntology:u}=s.apolloDataStore.ontologyManager;if(!u)throw new Error("featureTypeOntology is undefined");for(const[e,n]of o.entries())if(u.isTypeOf(c.type,"CDS")){const o=c.parent;if(!o)continue;const s=o.cdsLocations.find((e=>c.min===e.at(0)?.min&&c.max===e.at(-1)?.max));if(!s)continue;for(const o of s){const s=Wa(r.getFrame(o.min,o.max,c.strand??1,o.phase),a.bpPerPx),u=(a.bpToPx({refName:n.refName,coord:o.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,d=(o.max-o.min)/a.bpPerPx;za(t,i,a.displayedRegions[e].reversed?u-d:u,l,s,d)}}else{const o=Ha(c.strand,a.bpPerPx),r=(a.bpToPx({refName:n.refName,coord:c.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,s=c.length/a.bpPerPx;za(t,i,a.displayedRegions[e].reversed?r-s:r,l,o,s)}}),{name:"LinearApolloDisplayRenderSeqHighlight"}))}})))}(0,n);return l.views((e=>({contextMenuItems(t){const{apolloHover:n}=e;if(!n||!t)return[];const{topLevelFeature:a}=n;return e.getGlyph(a).getContextMenuItems(e)}}))).actions((e=>({startDrag(t,n,a){e.apolloDragging={start:t,current:t,feature:n,edge:a}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:a,feature:o,start:r}=e.apolloDragging;if(Math.abs(n.x-r.x)<=4)return e.setDragging(),void e.setCursor();const{displayedRegions:l}=e.lgv,s=e.getAssemblyId(l[r.regionNumber].assemblyName);let i;if("max"===a){const e=o._id;i=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[e],featureId:e,oldEnd:o.max,newEnd:n.bp,assembly:s})}else{const e=o._id;i=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[e],featureId:e,oldStart:o.min,newStart:n.bp,assembly:s})}e.changeManager.submit(i),e.setDragging(),e.setCursor()}}))).actions((e=>({onMouseDown(t){const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);Ga(n)?n.featureAndGlyphUnderMouse.glyph.onMouseMove(e,n,t):(e.setApolloHover(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setApolloHover();const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseUp(e,n,t),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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}=e;if(!a)return;const{glyph:o}=a;o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:i.types.optional(ra,{})}).named("LinearApolloDisplay")}const Va=a.ConfigurationSchema("LinearApolloSixFrameDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0});let Xa=null,Ka=null,Ya=null,Za=null;if("document"in globalThis)for(const e of["forward","backward"])for(const t of["light","dark"]){const n=document.createElement("canvas"),a=10;n.width=n.height=a;const o=n.getContext("2d");if(o){const r="light"===t?"rgba(0,0,0,0)":"rgba(0,0,0,0.75)",l="light"===t?"rgba(255,255,255,0.25)":"rgba(0,0,0,0.50)",s="forward"===e?o.createLinearGradient(0,a,a,0):o.createLinearGradient(0,0,a,a);s.addColorStop(0,r),s.addColorStop(.25,r),s.addColorStop(.25,l),s.addColorStop(.5,l),s.addColorStop(.5,r),s.addColorStop(.75,r),s.addColorStop(.75,l),s.addColorStop(1,l),o.fillStyle=s,o.fillRect(0,0,10,10),"forward"===e?"light"===t?Xa=o.createPattern(n,"repeat"):Ya=o.createPattern(n,"repeat"):"light"===t?Ka=o.createPattern(n,"repeat"):Za=o.createPattern(n,"repeat")}}function Qa(e,t){for(const n of e)if(ge.default(n,t))return!0;return!1}function eo(e,t,n,a){const{session:o}=a,{apolloDataStore:l}=o,{featureTypeOntology:s}=l.ontologyManager;if(!s)throw new Error("featureTypeOntology is undefined");const 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to={draw:function(e,t,n,a,o){const{apolloRowHeight:l,lgv:s,session:i,theme:c,highestRow:u}=a,{bpPerPx:d,displayedRegions:f,offsetPx:m}=s,g=f[o],{refName:h,reversed:y}=g,b=l,S=Math.round(.6*b),w=Math.round(.7*b),{children:v,min:E,strand:C,_id:x}=t;if(!v)return;const{apolloSelectedFeature:T}=i,{apolloDataStore:A}=i,{featureTypeOntology:N}=A.ontologyManager;if(!N)throw new Error("featureTypeOntology is undefined");const F=(s.bpToPx({refName:h,coord:E,regionNumber:o})?.offsetPx??0)-m,k=t.length/d,D=y?F-k:F,R=(1==C?3:4)*b,M=Math.round(.7*b);e.fillStyle=c?.palette.text.primary??"black",e.fillRect(D,R,k,M),e.fillStyle=p.alpha(T&&x===T._id?"rgb(0,0,0)":c?.palette.background.paper??"#ffffff",.7),e.fillRect(D+1,R+1,k-2,M-2);const I="dark"===c?.palette.mode?Ya:Xa,P="dark"===c?.palette.mode?Za:Ka,q=y?-1:1;let L=null,B=null;C&&([L,B]=C*q==1?[I,P]:[P,I]),L&&B&&(e.fillStyle=L,e.fillRect(D+1,R+1,k-2,(M-2)/2),e.fillStyle=B,e.fillRect(D+1,R+(M-2)/2,k-2,(M-2)/2));const O=new Set;for(const[,t]of v){if(!N.isTypeOf(t.type,"transcript")&&!N.isTypeOf(t.type,"pseudogenic_transcript"))continue;const{children:n,cdsLocations:a,_id:l}=t;if(n){for(const[,t]of n){if(!N.isTypeOf(t.type,"exon"))continue;const n=(s.bpToPx({refName:h,coord:t.min,regionNumber:o})?.offsetPx??0)-m,a=t.length/d,r=y?n-a:n,l=R+(M-S)/2;e.fillStyle=c?.palette.text.primary??"black",e.fillRect(r,l,a,S),a>2&&(e.clearRect(r+1,l+1,a-2,S-2),e.fillStyle=T&&t._id===T._id?"rgb(0,0,0)":p.alpha("#f5f500",.6),e.fillRect(r+1,l+1,a-2,S-2),L&&B&&(e.fillStyle=L,e.fillRect(r+1,l+1,a-2,(S-2)/2),e.fillStyle=B,e.fillRect(r+1,l+1+(S-2)/2,a-2,(S-2)/2)))}for(const n of a){let a=0,i=0,f=1;for(const g of n.sort(((e,t)=>e.max-t.max)))if(T&&N.isTypeOf(T.type,"CDS")&&l===T.parent?._id||!Qa(O,g)){const n=(g.max-g.min)/d,p=(s.bpToPx({refName:h,coord:g.min,regionNumber:o})?.offsetPx??0)-m,S=y?p-n:p;e.fillStyle=c?.palette.text.primary??"black";const v=r.getFrame(g.min,g.max,t.strand??1,g.phase),E=((v<0?-1*v+5:v)-1)*b+(b-w)/2;if(e.fillRect(S,E,n,w),n>2){e.clearRect(S+1,E+1,n-2,w-2);const t=c?.palette.framesCDS.at(v)?.main,o=t??"rgb(171,71,188)";if(e.fillStyle=o,e.fillStyle=T&&N.isTypeOf(T.type,"CDS")&&l===T.parent?._id?"rgb(0,0,0)":o,e.fillRect(S+1,E+1,n-2,w-2),f>1){const t=[(S-i)/2+i,Math.max(v<0?b*u+1:1,Math.min(a,E)-b/2)];e.strokeStyle="rgb(0, 128, 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c=e.getFeatureLayoutPosition(i);if(!c)return;const{layoutIndex:u}=c,{bpPerPx:d,displayedRegions:f,offsetPx:m}=o,g=f[u],{refName:h,reversed:y}=g,b=a,S=Math.round(.7*b);let w="Loc: ";const{strand:v}=i,{max:E,min:C,phase:x}=s;w+=`${C+1}–${E}`;let T=(o.bpToPx({refName:h,coord:y?E:C,regionNumber:u})?.offsetPx??0)-m;const A=r.getFrame(C,E,v??1,x),N=((A<0?-1*A+5:A)-1)*b+(b-S)/2,F=(E-C)/d,k=`Type: ${s.type}`,{attributes:D}=i,R=D.get("gff_name")?.find((e=>""!==e)),M=[t.measureText(k).width,t.measureText(w).width];R&&M.push(t.measureText(`Parent Type: ${i.type}`).width,t.measureText(`Parent Name: ${R}`).width);const I=Math.max(...M);T=T+F+5,t.fillStyle=p.alpha(l?.palette.text.primary??"rgb(1, 1, 1)",.7),t.fillRect(T,N,I+4,4===M.length?55:35),t.beginPath(),t.moveTo(T,N),t.lineTo(T-5,N+5),t.lineTo(T,N+10),t.fill(),t.fillStyle=l?.palette.background.default??"rgba(255, 255, 255)";let P=N+12;t.fillText(k,T+2,P),R&&(P+=12,t.fillText(`Parent Type: ${i.type}`,T+2,P),P+=12,t.fillText(`Parent Name: 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o)if(a.isTypeOf(e.type,"transcript")){const{cdsLocations:t,strand:n,children:o}=e;if(o)for(const[,e]of o){if(!a.isTypeOf(e.type,"exon"))continue;const t=1==e.strand?4:5,n=l.get(t);n?.push({rowNum:t,feature:e,cds:null})}for(const a of t)for(const t of a){let a=r.getFrame(t.min,t.max,n??1,t.phase);a=a<0?-1*a+5:a,l.get(a)||l.set(a,[]);const o=l.get(a);o?.push({rowNum:a,feature:e,cds:t})}}}}return l}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const[n,a]of t.entries())for(const[,t]of a)for(const{feature:a}of t)if(e._id===a._id)return{layoutIndex:n,layoutRow:0,featureRow:0}}}))).views((e=>({get highestRow(){return 5}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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),o=a?.features;if(o)for(const[,n]of 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n;const{feature:c,cds:u}=i,{topLevelFeature:d}=c,f=e.getGlyph(c);return{...n,featureAndGlyphUnderMouse:{cds:u,feature:c,topLevelFeature:d,glyph:f}}}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");n.stopPropagation(),e.apolloDragging={...e.apolloDragging,current:t}},setDragging(t){e.apolloDragging=t??null}}))).actions((e=>({setApolloHover(t){e.apolloHover=t},setCursor(t){e.cursor!==t&&(e.cursor=t)}}))).actions((()=>({onClick(){}})))}(0,n);return l.views((e=>({contextMenuItems(t){const{apolloHover:n}=e;if(!n||!t)return[];const{topLevelFeature:a}=n;return e.getGlyph(a).getContextMenuItems(e)}}))).actions((e=>({startDrag(t,n,a){e.apolloDragging={start:t,current:t,feature:n,edge:a}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:a,feature:o,start:r}=e.apolloDragging;if(Math.abs(n.x-r.x)<=4)return e.setDragging(),void 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n=e.getMousePosition(t);no(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseUp(e,n,t),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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}=e;if(!a)return;const{glyph:o}=a;o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloSixFrameDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:i.types.optional(ra,{})}).named("LinearApolloSixFrameDisplay")}const oo=a.ConfigurationSchema("ApolloPlugin",{ontologies:i.types.array(yt),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"}});function ro(e){if("LinearPileupDisplay"!==e.name)return e;const{stateModel:n}=e,a=n.views((e=>({getFirstRegion:()=>r.getContainingView(e).dynamicBlocks.contentBlocks[0],getAssembly(){const t=e.getFirstRegion(),n=r.getSession(e),{assemblyManager:a}=n,{assemblyName:o}=t,l=a.get(o);if(!l)throw new Error(`Could not find assembly named ${o}`);return l},getRefSeqId(t){const n=e.getFirstRegion(),{refName:a}=n,{refNameAliases:o}=t;if(!o)throw new Error(`Could not find aliases for ${t.name}`);const r=[...Object.entries(o)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t}))),l=r.find((e=>e.name===a))?._id;if(!l)throw new Error(`Could not find refSeqId named ${a}`);return l},createFeature(){const t=e.contextMenuFeature,n=e.getAssembly(),a=e.getRefSeqId(n),o=(t.get("CIGAR").toUpperCase().match(/\d+\D/g)??[]).map((e=>[(/\D/.exec(e)??[])[0],Number.parseInt(e,10)]));let r=0;const l=t.get("start");let s;const i=[];for(const[e,t]of o)"M"===e||"="===e?void 0===s&&(s=r+l):"N"===e&&void 0!==s&&(i.push({start:s,end:r+s}),s=void 0),"I"!==e&&(r+=t);void 0!==s&&i.push({start:s,end:r+l});const c={_id:ue.default().toHexString(),refSeq:a,min:t.get("start"),max:t.get("end"),type:"mRNA",strand:t.get("strand")};if(0===i.length)return c;c.children={};const[u]=i,d={_id:ue.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"CDS",strand:t.get("strand")};if(c.children[d._id]=d,1===i.length){const e={_id:ue.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"exon",strand:t.get("strand")};return c.children[e._id]=e,c}for(const e of i){d.min=Math.min(d.min,e.start),d.max=Math.max(d.max,e.end);const{end:n,start:o}=e,r={_id:ue.default().toHexString(),refSeq:a,min:o,max:n,type:"exon",strand:t.get("strand")};c.children[r._id]=r}return c},async onPileupFeatureContext(){const n=e.createFeature(),a=e.getAssembly(),o=new t.AddFeatureChange({changedIds:[n._id],typeName:"AddFeatureChange",assembly:a.name,addedFeature:n}),l=r.getSession(e);await l.apolloDataStore.changeManager.submit(o),l.notify("Annotation added 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n?n[0]:e.type},uo=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)return co(e);let a="";n.isTypeOf(e.type,"gene")&&(a="gene_name"),n.isTypeOf(e.type,"transcript")&&(a="transcript_name");const{attributes:o}=e,r=o?.[a];return r?r[0]:co(e)};function fo({annotationFeature:e,assembly:n,handleClose:a,refSeqId:o,session:r}){const l=r,s=y.useMemo((()=>Object.keys(e.children??{})),[e]),c=y.useMemo((()=>{for(const[,e]of l.apolloDataStore.assemblies)if(e._id===n.name)for(const[,t]of e.refSeqs)if(t._id===o)return t.features;return[]}),[]),[u,d]=y.useState(!0),[f,m]=y.useState(s),[g,h]=y.useState(""),[b,S]=y.useState([]),[w,v]=y.useState();return y.useEffect((()=>{h("");let t=[],n=[];if(e.children){const a=Object.values(e.children).filter((e=>io(e,l))).filter((e=>f.includes(e._id)));t=a.map((e=>e.min)),n=a.map((e=>e.max))}const{featureTypeOntology:a}=l.apolloDataStore.ontologyManager;a&&a.isTypeOf(e.type,"transcript")&&(t=[e.min,...t],n=[e.max,...n]);const 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c?de.default.createElement("div",{className:s.shading,ref:b,style:{height:u}},de.default.createElement(vo,{model:e,...t})):de.default.createElement("div",{className:s.details,style:{height:u}},de.default.createElement(oa,{model:e}))})),Fo=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 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this.revert(e);r.getSession(this.dataStore).notify("No changes to undo!","warning")}}class Ro extends ko{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 l=o.toString(),s=await this.fetch(n,l);if(!s.ok){const e=await je(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:l}=e,{assemblyManager:s}=r.getSession(this.clientStore),i=s.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=a.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(l),end:String(n)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await je(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),l=`${t}-${n}`,s=new Do(this.clientStore);o.hasListeners(l)||o.on(l,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===l){const n=e.Change.fromJSON(t.changeInfo);await s.submit(n,{submitToBackend:!1})}}))}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:l,refName:s,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=a.getConf(u,["sequence","metadata"]),f=d[s];if(!f)throw new Error(`Could not find refSeq "${s}"`);if(n)return{seq:await n,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,s));const p=g.getSequence(i,l);if(p.length===l-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(l)});b.search=S.toString();const w=b.toString(),v=this.getSeqFromServer(h,w,g,i,l);this.inFlight.set(t,v);const E=await v;return this.checkSocket(o,s,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 l=await r.text();return n.addSequence({sequence:l,start:a,stop:o}),l}async getRefNameAliases(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),l=new URLSearchParams({assembly:e});o.search=l.toString();const s=o.toString(),i=await this.fetch(n,s);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),l=new URLSearchParams({assembly:e});o.search=l.toString();const s=o.toString(),i=await this.fetch(n,s);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 n=a.getConf(t,["sequence","metadata"]);return!(!(n&&n.apollo&&n.internetAccountConfigId)||e&&n.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,l=new URL("changes",r).href,s=await this.fetch(o,l,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!s.ok){const e=await je(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class Mo extends ko{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 l=r.refSeqs.get(a);return l?{seq:l.getSequence(o,n),refSeq:a}:{seq:"",refSeq:a}}async getRefNameAliases(e){const t=this.clientStore.assemblies.get(e),n=[];if(!t)return n;for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getRegions(e){const t=this.clientStore.assemblies.get(e);if(!t)return[];const n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){const{clientStore:a}=this,{assemblies:o}=a;a.clearCheckResults();for(const[,e]of o)if("InMemoryFileDriver"===e.backendDriverType){const t=await Oe(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class Io extends ko{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:o}=a.getConf(n,["sequence","metadata"]),l=require("node:fs");return Be(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=(await this.getAssembly(t)).refSeqs.get(a);if(!r)throw new Error(`refSeq ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(n){if(!e.isAssemblySpecificChange(n))throw new Error(`Cannot use this type of change with local file: "${n.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),l=o.get(n.assembly);if(!l)throw new Error(`Could not find assembly with name "${n.assembly}"`);const{file:s}=a.getConf(l,["sequence","metadata"]),c=this.clientStore.assemblies.get(n.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${n.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 Oe(c);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=re.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function Po(e,n){const o=new AbortController,{signal:l}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",H.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map(H.ApolloAssembly),checkResults:i.types.map(H.CheckResult),ontologyManager:i.types.optional(pt,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):i.getParentOfType(n,H.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Do(e),collaborationServerDriver:new Ro(e),inMemoryFileDriver:new Mo(e),desktopFileDriver:r.isElectron?new Io(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,s.autorun((()=>{const{ontologyManager:t,pluginConfiguration:n}=e,o=n.ontologies;for(const n of o||[]){const[o,l,s,i]=[a.readConfObject(n,"name"),a.readConfObject(n,"version"),a.readConfObject(n,"source"),a.readConfObject(n,"textIndexFields")];if(!t.findOntology(o)){const n=r.getSession(e),{jobsManager:a}=n,c=new AbortController,u=`Loading ontology "${o}"`,d={name:u,statusMessage:`Loading ontology "${o}", version "${l}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(),a.abortJob(d.name)}};t.addOntology(o,l,s,{textIndexing:{indexFields:i},update:(e,t)=>{0!==t?100!==t?a.update(u,e,t):a.done(d):a.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){if(!t)return e.collaborationServerDriver;const n=r.getSession(e),{assemblyManager:o}=n,l=o.get(t);if(!l)return e.collaborationServerDriver;const{file:s,internetAccountConfigId:i}=a.getConf(l,["sequence","metadata"]);return r.isElectron&&s?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,n){if(!(t??n))throw new Error("Must provide either assemblyName or internetAccountId");let o=n;if(t&&!o){const{assemblyManager:n}=r.getSession(e),l=n.get(t);if(!l)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=a.getConf(l,["sequence","metadata"]))}const{internetAccounts:l}=e,s=l.find((e=>e.internetAccountId===o));if(!s)throw new Error(`No InternetAccount found with config id ${n}`);return s}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:l}=n;let s=e.assemblies.get(r);s||(s=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=s.refSeqs.get(i.refSeq);c||(c=s.refSeqs.put({_id:i.refSeq,name:l,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:l,refName:s,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:s,sequence:[]})),u.addSequence({start:i,stop:l,sequence:o})}}))})))}(c),d=n.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(Fo,{})}).extend((()=>{const e=s.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,n){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${a.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...n?{baseURL:{uri:n,locationType:"UriLocation"}}:{}}}})},broadcastLocations(){const{internetAccounts:t}=i.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).actions((e=>({afterCreate:i.flow((function*(){const t=i.getSnapshot(e),{id:n,name:a}=t;i.applySnapshot(e,{name:a,id:n});const{internetAccounts:o,jbrowse:r}=i.getRoot(e);s.autorun((()=>{const t=[];for(const n of e.views){if("LinearGenomeView"!==n.type)return;const a=n;if(a.initialized){const{dynamicBlocks:n}=a;n.forEach((n=>{if(void 0!==n.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=n,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&t.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===t.length){for(const e of o)"baseURL"in e&&e.postUserLocation([]);return}const n=[];for(const e of o)if("baseURL"in e){for(const e of t)n.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(n)}}),{name:"ApolloSession"});for(const n of o){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:a}=n,o=new URL("jbrowse/config.json",a).href,s=n.getFetcher({locationType:"UriLocation",uri:o});let c,u;try{c=yield s(o,{signal:l})}catch(e){console.error(e);continue}if(c.ok){try{u=yield c.json()}catch(e){console.error(e);continue}i.applySnapshot(r,u),i.applySnapshot(e,t)}else{const e=yield je(c,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const n=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return n?.(o);const r=a.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...n?.(o)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c={...i.getSnapshot(o),trackId:r.slice(0,r.length-13)};for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:s?.tracks&&[...s.tracks,c]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(c)},icon:qe.default}]:[...n?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c=s?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:c}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:qe.default}]}}}));return i.types.snapshotProcessor(d,{postProcessor(e,t){e.apolloSelectedFeature=void 0;const n=Object.fromEntries(Object.entries(e.apolloDataStore.assemblies).filter((([,e])=>"InMemoryFileDriver"===e.backendDriverType)));if(e.apolloDataStore={typeName:"Client",assemblies:n,checkResults:{}},!t)return e;const{apolloDataStore:a}=t,{checkResults:o}=a;for(const[,t]of o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=i.getSnapshot(t))}return e}})}const qo="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Lo=new t.CDSCheck;e.checkRegistry.registerCheck(Lo.name,Lo),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends ae.default{name="ApolloPlugin";version="0.3.6";configurationSchema=oo;install(e){!function(e){e.addAdapterType((()=>new we.default({name:"ApolloSequenceAdapter",configSchema:on,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:an})))}(e),function(e){e.addAdapterType((()=>new we.default({name:"ApolloRefNameAliasAdapter",configSchema:en,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Qt})))}(e),function(e){e.addTextSearchAdapterType((()=>new o.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:ln,AdapterClass:rn,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new o.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:Tn,ReactComponent:xn})})),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloTranscriptDetails",{});return new o.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:An,ReactComponent:$n})})),e.addTrackType((()=>{const t=a.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:o.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new o.TrackType({name:"ApolloTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new o.InternetAccountType({name:"ApolloInternetAccount",configSchema:Le,stateModel:Yt(Le)}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloDisplay",configSchema:jn,stateModel:Ja(0,jn),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Ao}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:Va,stateModel:ao(0,Va),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:No}))),e.addToExtensionPoint("Core-extendSession",Po.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:oe.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[Tt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",ro),e.addToExtensionPoint("Core-extendPluggableElement",ho),qo||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:l}=n;switch(l){case"getSequence":{const{region:a}=n,{assemblyName:l}=a,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const i=s.getBackendDriver(l),{seq:c}=await i.getSequence(a);t.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a),i=await s.getRegions(a);t.workers[0].postMessage({apollo:o,messageId:r,regions:i});break}case"getRefNameAliases":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a),i=await s.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[Dt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[It,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Bt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[$t,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Log out",onClick:e=>{e.queueDialog((t=>[Mt,{session:e,handleClose:()=>{t()}}]))}}))}};
+"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@apollo-annotation/common"),t=require("@apollo-annotation/shared"),n=require("@jbrowse/core/Plugin"),a=require("@jbrowse/core/configuration"),o=require("@jbrowse/core/pluggableElementTypes"),r=require("@jbrowse/core/util"),l=require("@mui/icons-material/Add"),s=require("@mui/material"),i=require("mobx"),c=require("mobx-state-tree"),u=require("socket.io-client"),d=require("@mui/icons-material/AdminPanelSettings"),f=require("@mui/icons-material/Delete"),m=require("@mui/icons-material/Input"),g=require("@mui/icons-material/Person"),p=require("@mui/icons-material/Rule"),h=require("@mui/icons-material/Info"),y=require("@mui/icons-material/Link"),b=require("@mui/icons-material/RadioButtonChecked"),S=require("@mui/icons-material/RadioButtonUnchecked"),w=require("bson-objectid"),E=require("react"),C=require("tss-react/mui"),v=require("@gmod/gff"),x=require("@mui/x-data-grid"),T=require("@jbrowse/core/ui"),A=require("@mui/icons-material/Close"),F=require("mobx-react"),k=require("@jbrowse/core/util/types/mst"),D=require("idb/with-async-ittr"),N=require("@jbrowse/core/util/aborting"),R=require("jsonpath"),I=require("@jbrowse/core/util/io"),M=require("fast-deep-equal/es6"),L=require("file-saver"),q=require("@mui/material/Checkbox"),P=require("@mui/material/FormControlLabel"),O=require("@mui/material/LinearProgress"),_=require("nanoid"),B=require("@mui/icons-material/AccountCircle"),U=require("@jbrowse/core/pluggableElementTypes/AdapterType"),$=require("@jbrowse/core/data_adapters/BaseAdapter"),j=require("@jbrowse/core/util/rxjs"),G=require("@jbrowse/core/util/simpleFeature"),W=require("@jbrowse/core/TextSearch/BaseResults"),z=require("@mui/icons-material/ExpandMore"),H=require("@mui/icons-material/Edit"),V=require("@mui/icons-material/MoreHoriz"),J=require("@mui/icons-material/AddBox"),X=require("@apollo-annotation/mst"),K=require("@emotion/styled"),Z=require("@mui/icons-material/ContentCopy"),Y=require("@mui/icons-material/ContentCut"),Q=require("@mui/icons-material/Remove"),ee=require("@mui/icons-material/Clear"),te=require("@mui/icons-material/UnfoldLess"),ne=require("@mui/icons-material/SkipNextRounded"),ae=require("@mui/icons-material/SkipPreviousRounded"),oe=require("@jbrowse/core/util/tracks"),re=require("@mui/icons-material/ExpandLess"),le=require("@mui/icons-material/Error"),se=require("@mui/icons-material/Lock"),ie=require("@mui/icons-material/Download"),ce=require("@mui/icons-material/FactCheck"),ue=require("@mui/icons-material/FileOpen"),de=require("@mui/icons-material/Logout"),fe=require("@mui/icons-material/Redo"),me=require("@mui/icons-material/TrackChanges"),ge=require("@mui/icons-material/Undo"),pe=require("@mui/icons-material/Save");function he(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}var ye=he(n),be=he(l),Se=he(d),we=he(f),Ee=he(m),Ce=he(g),ve=he(p),xe=he(h),Te=he(y),Ae=he(b),Fe=he(S),ke=he(w),De=he(E),Ne=he(v),Re=he(A),Ie=he(R),Me=he(M),Le=he(q),qe=he(P),Pe=he(O),Oe=he(B),_e=he(U),Be=he(G),Ue=he(W),$e=he(z),je=he(H),Ge=he(V),We=he(J),ze=he(K),He=he(Z),Ve=he(Y),Je=he(Q),Xe=he(ee),Ke=he(te),Ze=he(ne),Ye=he(ae),Qe=he(re),et=he(le),tt=he(se),nt=he(ie),at=he(ce),ot=he(ue),rt=he(de),lt=he(fe),st=he(me),it=he(ge),ct=he(pe);const ut=a.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:o.BaseInternetAccountConfig,explicitlyTyped:!0});async function dt(e,n,a){const o=Ne.default.parseStringSync(n,{parseSequences:!0,parseComments:!0,parseDirectives:!1,parseFeatures:!0});if(0===o.length)throw new Error("No features found in GFF3 file");let r=0,l=a.assemblies.get(e);l||(l=a.addAssembly(e,"InMemoryFileDriver"));for(const e of o)if(Array.isArray(e)){const n=t.gff3ToAnnotationFeature(e),a=l.refSeqs.get(n.refSeq)??l.addRefSeq(n.refSeq,n.refSeq);a.features.has(n._id)||a.addFeature(n)}else if("comment"in e)l.addComment(e.comment);else{r++;let t=l.refSeqs.get(e.id);t||(t=l.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===r)throw new Error("No embedded FASTA section found in GFF3");const s=await ft(l);return a.addCheckResults(s),l}async function ft(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(c.getSnapshot(t),((e,t)=>Promise.resolve(a.getSequence(e,t))));n.push(...e)}return n}function mt(e){const{attributes:t}=e,n=t.get("gff_name");return n?n[0]:""}function gt(e){const{attributes:t}=e,n=t.get("gff_id"),a=t.get("transcript_id"),o=t.get("exon_id"),r=t.get("protein_id");return n?n[0]:a?a[0]:o?o[0]:r?r[0]:""}function pt(e){const t=mt(e),n=gt(e);return t?`: ${t}`:n?`: ${n}`:""}function ht(e,t,n=!1){const a=[];a.push(e);for(const t of function(e){const t=[];let{parent:n}=e;for(;n;)t.push(n),({parent:n}=n);return t}(e))a.push(t);const o=function(e){const t=[];if(e.children)for(const[,n]of e.children)t.push(n);return t}(e);for(const e of o)e.min<t&&e.max>=t&&a.push(e);if(!n)return a;if(e.parent){const n=e.parent.children;if(n)for(const[,o]of n)o._id!=e._id&&o.min<t&&o.max>=t&&a.push(o)}return a}function yt(e,t,n,a){const o=a.bpToPx({refName:t,coord:e.min,regionNumber:n}),r=a.bpToPx({refName:t,coord:e.max,regionNumber:n});if(void 0===o||void 0===r)return;const{offsetPx:l}=a;return[o.offsetPx-l,r.offsetPx-l]}function bt(e,t,n){const[a,o]=n;if(!(Math.abs(o-a)<8))return Math.abs(a-t)<4?{feature:e,edge:"min"}:Math.abs(o-t)<4?{feature:e,edge:"max"}:void 0}function St(e,t){return Boolean(t&&e._id===t._id)}function wt(e,t){return!!t&&(e._id===t._id||e.hasDescendant(t._id))}function Et(e){let t;t=e.attributes.get("gff_name")?e.attributes.get("gff_name")?.join(","):e.attributes.get("gff_id")?e.attributes.get("gff_id")?.join(","):e._id;const n=`(${(e.min+1).toLocaleString("en")}..${e.max.toLocaleString("en")})`;if(t&&t.length+n.length>65){const e=60-n.length;t=e>0?t.slice(0,e):"",t=`${t}[...]`}return`${t} ${n}`}function Ct(e,t){const{apolloInternetAccount:n,changeManager:a,regions:o,selectedFeature:r,session:l}=e,s=[],i=n?n.role:"admin",c="admin"===i,u=!(i&&["admin","user"].includes(i)),[d]=o,f=e.getAssemblyId(d.assemblyName),m=e.getAssemblyId(d.assemblyName);return s.push({label:Et(t),type:"subHeader"},{label:"Add child feature",disabled:u,onClick:()=>{l.queueDialog((e=>[fn,{session:l,handleClose:()=>{e()},changeManager:a,sourceFeature:t,sourceAssemblyId:f,internetAccount:n}]))}},{label:"Copy features and annotations",disabled:u,onClick:()=>{l.queueDialog((e=>[yn,{session:l,handleClose:()=>{e()},changeManager:a,sourceFeature:t,sourceAssemblyId:m}]))}},{label:"Delete feature",disabled:!c,onClick:()=>{l.queueDialog((n=>[Sn,{session:l,handleClose:()=>{n()},changeManager:a,sourceFeature:t,sourceAssemblyId:m,selectedFeature:r,setSelectedFeature:t=>{e.setSelectedFeature(t)}}]))}}),s}function vt(e,t,n){const a=(e.max-e.min)*t,o=Math.max(e.min-a,1),r=Math.min(e.max+a,n);return{refName:e.refSeq,start:o,end:r}}function xt(e,t,n){const a=[{featureId:e._id,oldLocation:e[n],newLocation:t}],{parent:o}=e;return o&&("min"===n&&o[n]>t||"max"===n&&o[n]<t)&&a.push(...xt(o,t,n)),a}function Tt(e,t,n,a,o){const r=e._id,l=[{featureId:r,oldLocation:e[n],newLocation:t}],{parent:s,children:i}=e;if(i)for(const[,e]of 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${e.palette.divider}`,"&:not(:last-child)":{borderBottom:0}},accordionSummary:{flexDirection:"row-reverse"},accordionDetails:{padding:e.spacing(2),borderTop:"1px solid rgba(0, 0, 0, .125)"},radioIcon:{color:e.palette.tertiary.contrastText},dialog:{minWidth:550,maxWidth:800}})));function Lt(e,t,n,a,o,r,l,s,i){return!(!e||!(t&&a||n===It.GFF3&&a||a&&o&&r||l&&s&&i))}function qt({changeManager:e,handleClose:n,session:o}){const{classes:r}=Mt(),{internetAccounts:l}=c.getRoot(o),{notify:i}=o,u=l.filter((e=>"ApolloInternetAccount"===e.type));if(0===u.length)throw new Error("No Apollo internet account found");const[d,f]=E.useState(""),[m,g]=E.useState(""),[p,h]=E.useState(!1),[y,b]=E.useState(It.BGZIP_FASTA),[S,w]=E.useState(!0),[C,v]=E.useState(!1),[x,T]=E.useState(!1),[A,F]=E.useState(null),[k,D]=E.useState(null),[N,R]=E.useState(null),[I,M]=E.useState(""),[L,q]=E.useState(""),[P,O]=E.useState(""),[_,B]=E.useState(!1),[U,$]=E.useState(!1);async function j(e,t){const{jobsManager:n}=o,a=new AbortController,[{baseURL:r,getFetcher:l}]=u,s=new URL("files",r);s.searchParams.set("type",t);const i=s.href,c=new FormData;let f=e.name;t===It.FAI||t===It.GZI?f=`${f}.txt`:U&&!e.name.toLocaleLowerCase().endsWith(".gz")?f=`${f}.gz`:!U&&e.name.toLocaleLowerCase().endsWith(".gz")&&(f=`${f}.txt`),c.append("file",e,f),c.append("type",t);const m=l({locationType:"UriLocation",uri:i});if(m){const t={name:`UploadAssemblyFile for ${d}`,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{a.abort(),n.abortJob(t.name)}};n.runJob(t),n.update(t.name,`Uploading ${e.name}, this may take awhile`);const{signal:o}=a,r=await m(i,{method:"POST",body:c,signal:o});if(!r.ok){const e=await Dt(r,"Error when inserting new assembly (while uploading file)");return n.abortJob(t.name,e),g(e),""}const l=(await r.json())._id;return n.done(t),l}throw new Error("Failed to fetch")}E.useEffect((()=>{q(I?`${I}.fai`:"")}),[I]),E.useEffect((()=>{O(I?`${I}.gzi`:"")}),[I]),E.useEffect((()=>{$(!C&&y!==It.GFF3||!!A?.name.toLocaleLowerCase().endsWith(".gz"))}),[A,C,y]);let G=!1;try{const e=new URL(I);"http:"!==e.protocol&&"https:"!==e.protocol||(G=!0)}catch{}let W=!1;try{const e=new URL(L);"http:"!==e.protocol&&"https:"!==e.protocol||(W=!0)}catch{}let z=!1;try{const e=new URL(P);"http:"!==e.protocol&&"https:"!==e.protocol||(z=!0)}catch{}const[H,V]=De.default.useState("panelFastaInput"),J=e=>(t,n)=>{n&&V(e),$("panelGffInput"!==e)};return De.default.createElement(Rt,{open:!0,handleClose:n,"data-testid":"add-assembly-dialog",title:"Add new assembly",maxWidth:!1},De.default.createElement("form",{onSubmit:async function(a){let o;if(a.preventDefault(),g(""),T(!0),B(!0),i(`Assembly "${d}" is being added`,"info"),n(),a.preventDefault(),y===It.EXTERNAL)o=new t.AddAssemblyFromExternalChange({typeName:"AddAssemblyFromExternalChange",assembly:(new ke.default).toHexString(),assemblyName:d,externalLocation:{fa:I,fai:L,gzi:P}});else{if(!A)throw new Error("Missing fasta file");if(y===It.GFF3&&S){const e=await j(A,It.GFF3);o=new t.AddAssemblyAndFeaturesFromFileChange({typeName:"AddAssemblyAndFeaturesFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else if(y===It.GFF3){const e=await j(A,It.GFF3);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else if(C){const e=await j(A,It.FASTA);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else{if(!k||!N)throw new Error("Missing fasta index files");const e=await j(A,It.BGZIP_FASTA),n=await j(k,It.FAI),a=await j(N,It.GZI);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new 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Does not copy the files to the Apollo collaboration server, so ensure the URLs are stable.",placement:"top-start"},De.default.createElement(s.IconButton,{size:"small"},De.default.createElement(xe.default,{sx:{fontSize:18}}))))}),De.default.createElement(s.FormControlLabel,{"data-testid":"sequence-is-editable-checkbox",control:De.default.createElement(s.Checkbox,{onChange:()=>{v(!C)}}),checked:C,disabled:y===It.EXTERNAL,label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},"Store sequence in database",De.default.createElement(s.Tooltip,{title:"Enables users to edit the genomic sequence, but comes with performance impacts. 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e.replace(a,String(n));return e}const Ut="$PREFIXED_ID";function $t(e,t,n){return t===Ut?[Bt(e.id,n)]:Ie.default.query(e,t)}function jt(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!_t.has(e)))}function*Gt(e){for(const t of e)yield*jt(t)}function*Wt(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=Ie.default.query(t,"$..*");yield*Wt(e)}}function*zt(e,t,n){for(const a of t){const t=$t(e,a,n);if(t.length>0)for(const e of Gt(Wt(t)))yield[a,e]}}async function Ht(e,t,n){const a=await this.db,o=t??a.transaction(["nodes"]);N.checkAbortSignal(n);const r=[...jt(e)],l=[],s=new Map;l.push(...r.map((async(e,t)=>{N.checkAbortSignal(n);const a=o.objectStore("nodes").index("full-text-words");for await(const o of a.iterate(IDBKeyRange.bound(e,`${e}￿`,!1,!1))){N.checkAbortSignal(n);const e=o.value,a=s.get(e.id)??[e,new Set];a[1].add(t),s.set(e.id,a)}}))),await Promise.all(l),N.checkAbortSignal(n);const i=[];for(const[,[e,t]]of 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yn({changeManager:e,handleClose:n,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:i}=o,u=i.assemblyList,[d,f]=E.useState(u.find((e=>e.name!==r))?.name),[m,g]=E.useState([]),[p,h]=E.useState(""),[y,b]=E.useState(l.min),[S,w]=E.useState("");function C(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=C(a,t);e.refSeq=p,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),o="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:a,children:e.children&&n,_id:o}}return E.useEffect((()=>{h(""),async function(){if(!d)return void w("No assemblies to copy to");const e=await i.waitForAssembly(d);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const n=[...Object.entries(t)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t})));g(n),h(n[0]?._id||"")}().catch((e=>{w(String(e))}))}),[d,i]),De.default.createElement(Rt,{open:!0,title:"Copy features and 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0===r&&l(S[0])}),[S,r]),De.default.createElement(Rt,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},De.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),g(!0),u(""),!r)return void u("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:r.name});await e.submit(o,{internetAccountId:h.internetAccountId}),n(),a.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},p.length>1?De.default.createElement(De.default.Fragment,null,De.default.createElement(s.DialogContentText,null,"Select account"),De.default.createElement(s.Select,{value:h.internetAccountId,onChange:function(e){g(!1);const t=p.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID 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t)if(a._id!==e._id&&a.min>=e.min){n=a.min;break}if(n&&n!=e.parent.min)return{typeName:"LocationStartChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.min,newLocation:n}}if(e.max===n[0].max){let t;for(const a of n)if(a._id!=e._id&&a.max<=e.max){t=a.max;break}if(t&&t!=e.parent.max)return{typeName:"LocationEndChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.max,newLocation:t}}}return De.default.createElement(Rt,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature"},De.default.createElement("form",{onSubmit:o=>{!async function(o){o.preventDefault(),d(""),a?._id===i._id&&r();const s=[],u=new t.DeleteFeatureChange({changedIds:[i._id],typeName:"DeleteFeatureChange",assembly:l,changes:[{deletedFeature:c.getSnapshot(i),parentFeatureId:i.parent?._id}]});if(m&&(m.isTypeOf(i.type,"transcript")||m.isTypeOf(i.type,"pseudogenic_transcript"))){const e=g(i);e&&s.push(e)}if(m&&m.isTypeOf(i.type,"exon")){const e=function(e){if(!m)return;if(!m.isTypeOf(e.type,"exon"))return;if(!e.parent?.cdsLocations||0===e.parent.cdsLocations.length||0===e.parent.cdsLocations[0].length)return;if(!e.parent.children)throw new Error("Unable to find parent of CDS");if(1!=e.parent.cdsLocations.length)throw new Error("Unable to handle a transcript with multiple CDSs");const n=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let a;for(const t of e.parent.children.values())if(t.type===n[0].type){a=t;break}if(!a)throw new Error("Unable to find CDS");const o=n[0].min,r=n[n.length-1].max;if(!(e.min>o&&e.max<r||e.max<o||e.min>r)){if(e.min<=o&&e.max>=r)return new t.DeleteFeatureChange({changedIds:[a._id],typeName:"DeleteFeatureChange",assembly:l,changes:[{deletedFeature:c.getSnapshot(a),parentFeatureId:a.parent?._id}]});if(e.min<=o&&e.max>o){let t;for(const a of n)if(a.min>e.max){t=a.min;break}if(!t)throw new Error("Error setting new CDS 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e.children)a._id!=n.featureId&&a.max>t&&(t=a.max);t!=e.max&&s.push({typeName:n.typeName,changedId:e._id,featureId:e._id,oldLocation:e.max,newLocation:t})}}}const f=function(e,n){if(0===e.length)return;const a=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[],changes:[],assembly:n}),o=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[],changes:[],assembly:n});for(const t of e)"LocationStartChange"===t.typeName&&(a.changedIds.push(t.changedId),a.changes.push({featureId:t.featureId,oldStart:t.oldLocation,newStart:t.newLocation})),"LocationEndChange"===t.typeName&&(o.changedIds.push(t.changedId),o.changes.push({featureId:t.featureId,oldEnd:t.oldLocation,newEnd:t.newLocation}));if(a.changedIds.length>0&&0===o.changedIds.length)return a;if(o.changedIds.length>0&&0===a.changedIds.length)return o;throw new Error("Unexpected list of changes")}(s,l);await e.submit(u),f&&await e.submit(f),n(),o.preventDefault()}(o)}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Are you sure you want to delete the selected feature?")),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit"},"Yes"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),u?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},u)):null)}function wn({handleClose:e,session:n}){const[o,r]=E.useState(!1),[l,i]=E.useState(),[u,d]=E.useState(""),{collaborationServerDriver:f,getInternetAccount:m,inMemoryFileDriver:g}=n.apolloDataStore,p=[...f.getAssemblies(),...g.getAssemblies()];return De.default.createElement(Rt,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3"},De.default.createElement("form",{onSubmit:async function(r){if(r.preventDefault(),d(""),!l)return void d("Must select assembly to download");const{internetAccountConfigId:s}=a.getConf(l,["sequence","metadata"]);s?await async function(e){if(!l)return void d("Must select assembly to download");const t=m(l.configuration.name,e),n=new URL("export/getID",t.baseURL),a=new URLSearchParams({assembly:l.name});n.search=a.toString();const r=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:r}),i=await s(r,{method:"GET"});if(!i.ok){const e=await Dt(i,"Error when exporting ID");return void d(e)}const{exportID:c}=await i.json(),u=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c,includeFASTA:o?"true":"false"});u.search=f.toString();const g=u.toString();window.open(g,"_blank")}(s):function(e){if(!l)return void d("Must select assembly to download");const{assemblies:n}=e.apolloDataStore,o=n.get(l.name),r=o?.refSeqs;if(!r)return void d(`No refSeqs found for assembly "${l.name}"`);const s=[{directive:"gff-version",value:"3"}],i=a.getConf(l,["sequence","adapter","features"]);for(const e of i){const{end:t,refName:n,start:a}=e;s.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of r){const{features:n}=e;if(n)for(const[,e]of n)s.push(t.annotationFeatureToGFF3(c.getSnapshot(e)))}for(const e of i){const{refName:t,seq:n}=e;s.push({id:t,description:"",sequence:n})}const u=Ne.default.formatSync(s),f=new Blob([u],{type:"text/plain;charset=utf-8"});L.saveAs(f,`${l.displayName??l.name}.gff3`)}(n),e()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Select assembly"),De.default.createElement(s.Select,{labelId:"label",value:l?.name??"",onChange:function(e){const 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En({changeManager:e,handleClose:n,session:o}){const{apolloDataStore:r}=o,[l,i]=E.useState(),[c,u]=E.useState(),[d,f]=E.useState(""),[m,g]=E.useState(!1),[p,h]=E.useState(),[y,b]=E.useState(!1),[S,w]=E.useState(!1),{collaborationServerDriver:C,getInternetAccount:v}=r,x=C.getAssemblies();return E.useEffect((()=>{c&&(async()=>{const{internetAccountConfigId:e}=a.getConf(c,["sequence","metadata"]),t=v(c.name,e);if(!t)throw new Error("No Apollo internet account found");const{baseURL:n}=t,o=new URL("features/count",n),r=new URLSearchParams({assemblyId:c.name});o.search=r.toString();const l=t.getFetcher({locationType:"UriLocation",uri:o.toString()});w(!0);const s=await l(o.toString(),{method:"GET"});if(!s.ok)throw new Error(await Dt(s));{const e=await s.json();h(e.count)}w(!1)})().catch((e=>{console.error(e),f(e.message??e)}))}),[v,o,c]),De.default.createElement(Rt,{open:!0,title:"Import Features from GFF3 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t.MergeExonsChange({changedIds:[l._id],typeName:"MergeExonsChange",assembly:r,firstExon:c.getSnapshot(l),secondExon:c.getSnapshot(d),parentFeatureId:i._id});e.submit(f),n(),s.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(m).length?"There are no neighbouring exons to merge with":"Merge with exon on:",De.default.createElement(s.FormControl,{style:{marginTop:5}},De.default.createElement(s.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",name:"radio-buttons-group",value:d,onChange:e=>{u("");const{value:t}=e.target;f(m[t])}},Object.keys(m).map((e=>De.default.createElement(s.FormControlLabel,{value:e,key:e,control:De.default.createElement(s.Radio,null),label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},Tn(e,m))})))))),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:0===Object.keys(m).length||void 0===d},"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),i?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},i)):null)}function Fn(e){let t;return t=e.attributes.get("gff_name")?e.attributes.get("gff_name")?.join(","):e.attributes.get("gff_id")?e.attributes.get("gff_id")?.join(","):e._id,`${t} [${e.min+1}-${e.max}]`}function kn({changeManager:e,handleClose:n,selectedFeature:a,session:o,setSelectedFeature:r,sourceAssemblyId:l,sourceFeature:i}){const[u,d]=E.useState(""),f=function(e,t){const n=e.parent;if(!n)throw new Error("Unable to find parent of reference transcript");const{featureTypeOntology:a}=t.apolloDataStore.ontologyManager;if(!a)throw new Error("featureTypeOntology is undefined");const o={};if(n.children)for(const[,t]of n.children)a.isTypeOf(t.type,"transcript")&&t._id!==e._id&&(o[t._id]=t);return o}(i,o),m=Object.keys(f).at(0),[g,p]=E.useState(m);return De.default.createElement(Rt,{open:!0,title:"Merge transcripts",handleClose:n,maxWidth:!1,"data-testid":"merge-transcripts"},De.default.createElement("form",{onSubmit:function(o){if(o.preventDefault(),d(""),!g)return;const s=f[g];if(a?._id===i._id&&r(),!i.parent)throw new Error("Cannot find parent");const u=new t.MergeTranscriptsChange({changedIds:[i._id],typeName:"MergeTranscriptsChange",assembly:l,firstTranscript:c.getSnapshot(i),secondTranscript:c.getSnapshot(s),parentFeatureId:i.parent._id});e.submit(u),n()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(f).length?"There are no transcripts to merge with":"Merge with 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Dn({handleClose:e,session:t}){const{apolloDataStore:n}=t,{addAssembly:a,addSessionAssembly:o,assemblyManager:l,notify:i}=t,[c,u]=E.useState(null),[d,f]=E.useState(""),[m,g]=E.useState(""),[p,h]=E.useState(!1),y=s.useTheme();return De.default.createElement(Rt,{open:!0,title:"Open local GFF3 file",handleClose:e,maxWidth:!1,"data-testid":"open-local-file"},De.default.createElement("form",{onSubmit:async function(s){if(s.preventDefault(),g(""),h(!0),!c)throw new Error("No file selected");const u=await new Response(c).text(),f=`${d}-${c.name}-${_.nanoid(8)}`;try{await dt(f,u,n)}catch(t){return console.error(t),i(`Error loading GFF3 ${c.name}, ${String(t)}`,"error"),void e()}const m={};if(r.isElectron){const{webUtils:e}=globalThis.require("electron");m.file=e.getPathForFile(c)}const 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function(t){if(!c.isAlive(e))return;const{baseURL:n,controller:a}=e,o=new URL("users/userLocation",n).href,r=new URLSearchParams(JSON.stringify(t)),l=e.getFetcher({locationType:"UriLocation",uri:o});try{if(!(await l(o,{method:"POST",body:r,signal:a.signal})).ok)throw new Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).actions((e=>({initialize:c.flow((function*(t){if("admin"===t){const t=c.getRoot(e);r.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:Se.default,subMenu:[{label:"Add Assembly",icon:be.default,onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:we.default,onClick:e=>{e.queueDialog((t=>[bn,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import 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da=C.makeStyles()((e=>({list:{"li:nth-of-type(odd)":{backgroundColor:e.palette.action.focus},"li:nth-of-type(even)":{backgroundColor:e.palette.action.hover}}}))),fa=F.observer((function({assembly:e,editable:n,feature:a,session:o}){const{pluginManager:l}=r.getEnv(o),{classes:u}=da(),[d,f]=E.useState(null),[m,g]=E.useState(null),[p,h]=E.useState(null),[y,b]=E.useState(!1),[S,w]=E.useState(),C=Boolean(d),{changeManager:v}=o.apolloDataStore,{notify:x}=o;function T(){f(null),g(null)}const{_id:A,attributes:F}=a,k=l.evaluateExtensionPoint("Apollo-AttributeEditorComponent",ca,{key:S});return De.default.createElement(De.default.Fragment,null,De.default.createElement(s.List,{className:u.list},i.entries(F).map((([r,i])=>{const u=l.evaluateExtensionPoint("Apollo-AttributeEditorComponent",ca,{key:r}),d=l.evaluateExtensionPoint("Apollo-AttributeViewerComponent",ua,{key:r});return 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t.FeatureAttributeChange({changedIds:[A],typeName:"FeatureAttributeChange",assembly:e,featureId:A,oldAttributes:a,newAttributes:r});v.submit(l)}(m),T()}},De.default.createElement(s.ListItemIcon,null,De.default.createElement(we.default,{fontSize:"small"})),De.default.createElement(s.Typography,{variant:"inherit"},"Delete")),De.default.createElement(s.MenuItem,{onClick:function(){m&&h(m),T()}},De.default.createElement(s.ListItemIcon,null,De.default.createElement(je.default,{fontSize:"small"})),De.default.createElement(s.Typography,{variant:"inherit"},"Edit"))))})),ma=F.observer((function({onChangeCommitted:e,value:t,...n}){const[a,o]=E.useState(String(t)),[r,l]=E.useState(!1),[i,c]=E.useState(null);E.useEffect((()=>{o(String(t))}),[t]),E.useEffect((()=>{r&&(i?.blur(),l(!1))}),[r,i]);const u=Number.isNaN(Number(a));return De.default.createElement(s.TextField,{...n,type:"text",onChange:function(e){o(e.target.value)},value:a,onKeyDown:e=>{"Enter"===e.key?i?.blur():"Escape"===e.key&&(o(String(t)),l(!0))},onBlur:()=>{const n=Number(a);a!==String(t)&&(Number.isNaN(n)?o(String(t)):e(n))},inputRef:e=>{c(e)},error:u,helperText:u?"Not a valid number":void 0})})),ga=F.observer((function({assembly:e,feature:n,session:a}){const[o,r]=E.useState(""),[l,i]=E.useState(""),{_id:c,assemblyId:u,max:d,min:f,strand:m,type:g}=n,p=e=>{a.notify(e.message,"error")},{changeManager:h}=a.apolloDataStore;function y(n){const{value:a}=n.target,o=a?Number(a):void 0,r=new t.StrandChange({typeName:"StrandChange",changedIds:[c],featureId:c,oldStrand:m,newStrand:o,assembly:e});return h.submit(r)}return De.default.createElement("div",{"data-testid":"basic_information"},De.default.createElement(ma,{margin:"dense",id:"start",label:"Start",fullWidth:!0,variant:"outlined",value:f+1,onChangeCommitted:function(n){n--;const a=new 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zo(e,t,n){const a=new Map;for(const t of e)(a.get(t.message)??a.set(t.message,[]).get(t.message)).push(t);const o=[];for(const[e,s]of a.entries()){if(0===s.length)continue;s.sort(((e,t)=>e.start-t.start));let a=[s[0]],i=s[0].start,c=s[0].start+t;const u=()=>{const t=a.map((e=>e.start)).sort(((e,t)=>e-t)),n=Math.floor(t.length/2),r=a[0].ids;o.push({_id:a[0]._id,message:e,start:t.length%2?t[n]:(t[n-1]+t[n])/2,count:a.length,members:[...a],range:{min:i,max:c},featureIds:r})};for(let e=1;e<s.length;e++){const o=s[e],d=o.start,f=d+t;r=c,l=d,(n?l<=r:l<r)?(a.push(o),d<i&&(i=d),f>c&&(c=f)):(u(),a=[o],i=d,c=f)}u()}var r,l;return o.sort(((e,t)=>e.message.localeCompare(t.message)||e.start-t.start)),o}function Ho(e,t,n){const a=[];for(let o=e;o<e+t;o++){const e=n.get(o);e&&a.push(e)}return a}function Vo(e,t){for(const n of e)for(const[e,a]of n)if(r.doesIntersect2(t.min,t.max,e,a)||r.doesIntersect2(e,a,t.min,t.max))return!1;return!0}function Jo(e,n){return function(e,n){return function(e,t){const 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n=e.getMousePosition(t);Ft(n)&&e.getGlyph(n.feature).onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);Ft(n)?e.getGlyph(n.feature).onMouseMove(e,n,t):(e.setHoveredFeature(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setHoveredFeature();const n=e.getMousePosition(t);Ft(n)&&e.getGlyph(n.feature).onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);Ft(n)?e.getGlyph(n.feature).onMouseUp(e,n,t):e.setSelectedFeature(),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){c.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,hoveredFeature:a}=e;if(!a)return;const o=e.getGlyph(a.feature);o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:c.types.optional(Qa,{})}).named("LinearApolloDisplay")}const Xo=a.ConfigurationSchema("LinearApolloReferenceSequenceDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0});function Ko(e,t){return t.palette.bases[e.toUpperCase()].main.toString()??"lightgray"}function Zo(e,t,n,a,o){const r=Math.min(n,10);e.fillStyle="#000",e.font=`${r}px`;const l=e.measureText(a).width;e.fillText(a,t+(n-l)/2,o+10)}function Yo(e,t,n,a,o,l,s,i,c,u,d,f){let m=s.slice(i,i+3).toUpperCase();c&&(m=function(e){return[...e].map((e=>r.revcom(e))).reverse().join("")}(m));const g=r.defaultCodonTable[m];if(!g)return;const 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o.BaseDisplay.named("BaseLinearApolloReferenceSequenceDisplay").props({type:c.types.literal("LinearApolloReferenceSequenceDisplay"),configuration:a.ConfigurationReference(t),showStartCodons:!1,showStopCodons:!0,highContrast:!1,heightPreConfig:c.types.maybe(c.types.refinement("displayHeight",c.types.number,(e=>e>=20))),sequenceRowHeight:15}).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...oe.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get lgv(){return r.getContainingView(e)}}))).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)})))},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>=3)return"Zoom in to see sequence"}}))).views((e=>({get apolloInternetAccount(){const[t]=e.regions,{internetAccounts:n}=c.getRoot(e),{assemblyName:o}=t,{assemblyManager:r}=e.session,l=r.get(o);if(!l)throw new Error(`No assembly found with name ${o}`);const{internetAccountConfigId:s}=a.getConf(l,["sequence","metadata"]);return n.find((e=>a.getConf(e,"internetAccountId")===s))},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},get hoveredFeature(){return e.session.apolloHoveredFeature},get height(){const{sequenceRowHeight:t}=e;return e.lgv.bpPerPx<=1?8*t:6*t}}))).volatile((()=>({scrollTop:0}))).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},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleHighContrast(){e.highContrast=!e.highContrast}}))).views((e=>{const{trackMenuItems:t}=e;return{trackMenuItems(){const{showStartCodons:n,showStopCodons:a,highContrast:o}=e;return[...t(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show start codons",type:"checkbox",checked:n,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:a,onClick:()=>{e.toggleShowStopCodons()}},{label:"Use high contrast colors",type:"checkbox",checked:o,onClick:()=>{e.toggleHighContrast()}}]}]}}})).actions((e=>({afterAttach(){c.addDisposer(e,i.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&e.lgv.bpPerPx<=3&&e.session.apolloDataStore.loadRefSeq(e.regions)}),{name:"LinearApolloReferenceSequenceDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return 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e.session.apolloHoveredFeature}}))).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},showGraphicalOnly(){e.graphical=!0,e.table=!1},showTableOnly(){e.graphical=!1,e.table=!0},showGraphicalAndTable(){e.graphical=!0,e.table=!0},toggleShowFeatureLabels(){e.showFeatureLabels=!e.showFeatureLabels},toggleShowCheckResults(){e.showCheckResults=!e.showCheckResults},updateFilteredFeatureTypes(t){e.filteredFeatureTypes=c.cast(t)},setZoomThresholdSetting({zoomThreshold:t}){e.zoomThreshold=t}}))).views((e=>{const{filteredFeatureTypes:t,trackMenuItems:n}=e;return{trackMenuItems(){const{graphical:a,table:o,showFeatureLabels:l,showCheckResults:s}=e;return[...n(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show graphical display",type:"radio",checked:a&&!o,onClick:()=>{e.showGraphicalOnly()}},{label:"Show table 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n=e.session;e.session.queueDialog((a=>[jo,{session:n,handleClose:()=>{a()},featureTypes:c.getSnapshot(t),onUpdate:t=>{e.updateFilteredFeatureTypes(t)}}]))}}]}}})).actions((e=>({setSelectedFeature(t){e.session.apolloSetSelectedFeature(t)},setHoveredFeature(t){e.session.apolloSetHoveredFeature(t)},showFeatureDetailsWidget(t,n){const[a]=e.regions,{assemblyName:o,refName:r}=a,l=e.getAssemblyId(o);if(!l)return;const{session:s}=e,{changeManager:i}=s.apolloDataStore,[c,u]=n??["ApolloFeatureDetailsWidget","apolloFeatureDetailsWidget"],d=s.addWidget(c,u,{feature:t,assembly:l,refName:r,changeManager:i});s.showWidget(d)},afterAttach(){c.addDisposer(e,i.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&(e.session.apolloDataStore.loadFeatures(e.regions),e.lgv.bpPerPx<=3&&e.session.apolloDataStore.loadRefSeq(e.regions))}),{name:"LinearApolloSixFrameDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return n.named("LinearApolloSixFrameDisplayLayouts").props({featuresMinMaxLimit:5e5}).volatile((()=>({seenFeatures:i.observable.map()}))).views((e=>({get featuresMinMax(){const{assemblyManager:t}=e.session;return e.lgv.displayedRegions.map((n=>{const a=t.get(n.assemblyName);let o,l;const{end:s,refName:i,start:c}=n;for(const[,t]of e.seenFeatures)i!==a?.getCanonicalRefName(t.refSeq)||!r.doesIntersect2(c,s,t.min,t.max)||t.length>e.featuresMinMaxLimit||(void 0===o&&({min:o}=t),void 0===l&&({max:l}=t),t.minWithChildren<o&&({min:o}=t),t.maxWithChildren>l&&({max:l}=t));if(void 0!==o&&void 0!==l)return[o,l]}))},getGlyph:e=>mr,featureLabelSpacer:t=>e.showFeatureLabels?2*t-1:t}))).actions((e=>({addSeenFeature(t){e.seenFeatures.set(t._id,t)},deleteSeenFeature(t){e.seenFeatures.delete(t)}}))).views((e=>({get geneTrackRowNums(){return[4,5].map((t=>e.featureLabelSpacer(t)))}}))).views((e=>({get featureLayouts(){const{assemblyManager:t}=e.session;return e.lgv.displayedRegions.map(((n,a)=>{const o=t.get(n.assemblyName),l=new Map;if(!e.featuresMinMax[a])return l;const{end:s,refName:i,start:u}=n;for(const[t,n]of e.seenFeatures.entries()){if(!c.isAlive(n)){e.deleteSeenFeature(t);continue}if(i!==o?.getCanonicalRefName(n.refSeq)||!r.doesIntersect2(u,s,n.min,n.max))continue;const{featureTypeOntology:a}=e.session.apolloDataStore.ontologyManager;if(!a)throw new Error("featureTypeOntology is undefined");if(n.looksLikeGene){const t=1==n.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1];l.get(t)||l.set(t,[]);const o=l.get(t);o?.push({rowNum:t,feature:n});const{children:s}=n;if(!s)continue;for(const[,t]of s)if(a.isTypeOf(t.type,"transcript")){const{cdsLocations:n,strand:o,children:s}=t;if(s)for(const[,t]of s){if(!a.isTypeOf(t.type,"exon"))continue;const n=1==t.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1],o=l.get(n);o?.push({rowNum:n,feature:t})}for(const a of n)for(const n of a){let a=r.getFrame(n.min,n.max,o??1,n.phase);a=e.featureLabelSpacer(a<0?-1*a+5:a),l.get(a)||l.set(a,[]);const s=l.get(a);s?.push({rowNum:a,feature:t})}}}}return l}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const[n,a]of t.entries())for(const[,t]of a)for(const{feature:a}of t)if(e._id===a._id)return{layoutIndex:n,layoutRow:0,featureRow:0}}}))).views((e=>({get highestRow(){return 5}}))).actions((e=>({afterAttach(){c.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),a=n?.getByRefName(t.refName),o=a?.features;if(o)for(const[,n]of o)r.doesIntersect2(t.start,t.end,n.min,n.max)&&!e.seenFeatures.has(n._id)&&e.addSeenFeature(n)}}),{name:"LinearApolloSixFrameDisplaySetSeenFeatures",delay:1e3}))}})))}(0,t).named("LinearApolloSixFrameDisplayRendering").props({apolloRowHeight:20,detailsMinHeight:200,detailsHeight:200,lastRowTooltipBufferHeight:120,isShown:!0,filteredTranscripts:c.types.array(c.types.string)}).volatile((()=>({canvas:null,overlayCanvas:null,collaboratorCanvas:null,theme:s.createTheme()}))).views((e=>({get featuresHeight(){return(e.highestRow+1)*e.apolloRowHeight*(e.showFeatureLabels?2:1)+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},setTheme(t){e.theme=t}}))).actions((e=>({afterAttach(){c.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 l of a){if(l.refSeq!==r.refName)continue;const{end:a,refSeq:s,start:i}=l,c=e.lgv.bpToPx({refName:s,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:"LinearApolloSixFrameDisplayRenderCollaborators"})),c.addDisposer(e,i.autorun((()=>{const{canvas:t,featureLayouts:n,featuresHeight:a,lgv:o}=e;if(!o.initialized||e.regionCannotBeRendered())return;const{displayedRegions:l,dynamicBlocks:s}=o,i=t?.getContext("2d");if(i){i.clearRect(0,0,s.totalWidthPx,a);for(const[t,a]of n.entries()){const n=l[t];for(const[o,l]of a.entries())for(const{feature:a}of l){if(!a.looksLikeGene)continue;if(!r.doesIntersect2(n.start,n.end,a.min,a.max))continue;const{topLevelFeature:l}=a,s=e.getGlyph(l);void 0!==s&&s.draw(i,l,o,e,t)}}}}),{name:"LinearApolloSixFrameDisplayRenderFeatures"}))}})))}(0,t);return n.named("LinearApolloSixFrameDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0}))).views((e=>({getMousePosition(t){const n=kt(t,e.lgv),{bp:a,regionNumber:o,y:l}=n,s=Math.floor(l/e.apolloRowHeight)+1,i=e.featureLayouts[o].get(s);if(!i)return n;const{featureTypeOntology:c}=e.session.apolloDataStore.ontologyManager;if(!c)throw new Error("featureTypeOntology is undefined");let u;if(e.geneTrackRowNums.includes(s)?(u=i.find((e=>"exon"==e.feature.type&&a>=e.feature.min&&a<=e.feature.max)),u||(u=i.find((e=>a>=e.feature.min&&a<=e.feature.max)))):u=i.find((t=>{const{feature:n}=t,o=n.attributes.get("gff_id")?.toString();if(!c.isTypeOf(n.type,"transcript"))return!1;for(const t of n.cdsLocations)for(const l of t){let t=r.getFrame(l.min,l.max,n.strand??1,l.phase);if(t=e.featureLabelSpacer(t<0?-1*t+5:t),s===t&&a>=l.min&&a<=l.max)return void 0===o||!e.filteredTranscripts.includes(o)}return!1})),!u)return n;const{feature:d}=u;return{...n,feature:d}}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in 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t.LocationEndChange({typeName:"LocationEndChange",changedIds:c.map((e=>e.featureId)),changes:c.map((e=>({featureId:e.featureId,oldEnd:e.oldLocation,newEnd:e.newLocation}))),assembly:i}):new t.LocationStartChange({typeName:"LocationStartChange",changedIds:c.map((e=>e.featureId)),changes:c.map((e=>({featureId:e.featureId,oldStart:e.oldLocation,newStart:e.newLocation}))),assembly:i});e.changeManager.submit(u),e.setDragging(),e.setCursor()}}))).actions((e=>({onMouseDown(t){const n=e.getMousePosition(t);Ft(n)&&e.getGlyph(n.feature).onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);Ft(n)?e.getGlyph(n.feature).onMouseMove(e,n,t):(e.setHoveredFeature(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setHoveredFeature();const n=e.getMousePosition(t);Ft(n)&&e.getGlyph(n.feature).onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);Ft(n)?e.getGlyph(n.feature).onMouseUp(e,n,t):e.setSelectedFeature(),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){c.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,hoveredFeature:a}=e;if(!a)return;const o=e.getGlyph(a.feature);o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloSixFrameDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:c.types.optional(Qa,{})}).named("LinearApolloSixFrameDisplay")}const pr=a.ConfigurationSchema("ApolloPlugin",{ontologies:c.types.array(ln),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"},hasRole:{description:"Flag used internally by jbrowse-plugin-apollo",type:"boolean",defaultValue:!1},backgroundColorForFeature:{description:"Color ",type:"string",defaultValue:"jexl:colorFeature(featureType)",contextVariable:["featureType"]}}),hr=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"gene")||n.isTypeOf(e.type,"transcript")||n.isTypeOf(e.type,"pseudogene")||n.isTypeOf(e.type,"pseudogenic_transcript")},yr=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"gene")||n.isTypeOf(e.type,"pseudogene")},br=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"transcript")||n.isTypeOf(e.type,"pseudogenic_transcript")};function Sr(e){const{attributes:t}=e,n=["gene_name","gene_id","gene_stable_id"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}const wr=e=>{const t=function(e){const{attributes:t}=e,n=["name","gff_name","transcript_name","gene_name"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}(e),n=function(e){const{attributes:t}=e,n=["id","gff_id","transcript_id","gene_id","gene_stable_id","stable_id"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}(e);return t?`${e.type} - ${t}`:n?`${e.type} - ${n}`:e.type};function Er({annotationFeature:e,assembly:n,handleClose:a,refSeqId:o,session:r,region:l}){const i=r,{featureTypeOntology:u}=i.apolloDataStore.ontologyManager,d=E.useMemo((()=>Object.keys(e.children??{})),[e]),[f,m]=E.useState(!0),[g,p]=E.useState(d),[h,y]=E.useState(""),[b,S]=E.useState([]),[w,C]=E.useState(!1),[v,x]=E.useState(),T=i.apolloDataStore.assemblies.get(n.name),A=T?.refSeqs.get(o),F=A?.getFeatures(l.start,l.end),k=()=>{const t=[];for(const n of F??[])if(!(n.min>l.end||n.max<l.start)&&u?.isTypeOf(n.type,"gene")&&n.strand===e.strand){const e=c.getSnapshot(n);t.push(e)}return t};E.useEffect((()=>{y("");const e=k();S(e),x(e[0])}),[g,f,l]);const D=async e=>{if(v)for(const a of Object.keys(e)){const o=new t.AddFeatureChange({parentFeatureId:v._id,changedIds:[v._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:e[a]});await I(o)}},N=async a=>{const r=(new ke.default).toHexString(),l=Math.min(...Object.values(a).map((e=>e.min))),s=Math.max(...Object.values(a).map((e=>e.max))),c=new t.AddFeatureChange({changedIds:[r],typeName:"AddFeatureChange",assembly:n.name,addedFeature:{_id:r,refSeq:o,min:l,max:s,strand:e.strand,type:"gene",children:a,attributes:{name:[Sr(e)],gene_name:[Sr(e)]}}});await I(c),i.apolloSetSelectedFeature(r)},R=async(e,a)=>{if(!v)return;const o=[];e!==v.min&&o.push(new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[v._id],featureId:v._id,assembly:n.name,oldStart:v.min,newStart:e})),a!==v.max&&o.push(new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[v._id],featureId:v._id,assembly:n.name,oldEnd:v.max,newEnd:a}));for(const e of o)await I(e)},I=async e=>{await i.apolloDataStore.changeManager.submit(e)};return De.default.createElement(Rt,{open:!0,title:"Create Apollo Annotation",handleClose:a,fullWidth:!0,maxWidth:"sm"},De.default.createElement(s.DialogTitle,{fontSize:15},"Select the feature to be copied to apollo track"),De.default.createElement(s.DialogContent,null,De.default.createElement(s.Box,{sx:{ml:3}},hr(e,i)&&De.default.createElement(s.FormControlLabel,{control:De.default.createElement(s.Checkbox,{size:"small",checked:f,onChange:e=>{const t=e.target.checked;m(t),p(t?d:[])}}),label:`${wr(e)} 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t=b.find((t=>t._id===e.target.value));x(t)},disabled:w},b.map((e=>De.default.createElement(s.MenuItem,{key:e._id,value:e._id},`${wr(e)} (${e.min+1}..${e.max})`)))))),De.default.createElement(s.Box,{sx:{ml:3}},De.default.createElement(s.FormGroup,null,De.default.createElement(s.FormControlLabel,{control:De.default.createElement(s.Checkbox,{checked:w,onChange:e=>{C(e.target.checked)}}),label:"Create new gene"}))))),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:0===g.length||!f&&g.length>0&&!v,onClick:async()=>{if(f){if(yr(e,i)&&(await(async()=>{let a;if(e.children&&g.length!==Object.values(e.children).length){const o={};for(const t of g)o[t]=e.children[t];a=new t.AddFeatureChange({changedIds:[e._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:{...e,children:o}})}else a=new t.AddFeatureChange({changedIds:[e._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:e});await 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e=r.getSession(this.dataStore),t=this.recentChanges.pop();if(t)return this.undoneChanges.push(t),this.undo(t);e.notify("No changes to undo!","info")}async redoLastChange(){const e=r.getSession(this.dataStore),t=this.undoneChanges.pop();if(t)return this.recentChanges.push(t),this.redo(t);e.notify("No changes to redo!","info")}}class Br extends Or{inFlight=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:a}=n,o=new URL("features/searchFeatures",a),r=new URLSearchParams({assemblies:t.join(","),term:e});o.search=r.toString();const l=o.toString(),s=await this.fetch(n,l);if(!s.ok){const e=await Dt(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:l}=e,{assemblyManager:s}=r.getSession(this.clientStore),i=s.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=a.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(l),end:String(n)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await Dt(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),l=`${t}-${n}`,s=new _r(this.clientStore);o.hasListeners(l)||o.on(l,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===l){const n=e.Change.fromJSON(t.changeInfo);e.isFeatureChange(n)&&this.haveDataForChange(n)&&await s.submit(n,{submitToBackend:!1})}}))}haveDataForChange(e){const{assembly:t,changedIds:n}=e;if(!this.clientStore.assemblies.get(t))return!1;for(const e of n)if(this.clientStore.getFeature(e))return!0;return!1}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:l,refName:s,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=a.getConf(u,["sequence","metadata"]),f=d[s];if(!f)throw new Error(`Could not find refSeq "${s}"`);if(n)return{seq:await n,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,s));const p=g.getSequence(i,l);if(p.length===l-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(l)});b.search=S.toString();const w=b.toString(),E=this.getSeqFromServer(h,w,g,i,l);this.inFlight.set(t,E);const C=await E;return this.checkSocket(o,s,h),this.inFlight.delete(t),{seq:C,refSeq:f}}async getSeqFromServer(e,t,n,a,o){const r=await this.fetch(e,t);if(!r.ok){let e;try{e=await r.text()}catch{e=""}throw new Error(`getSequence failed: ${r.status} (${r.statusText})${e?` (${e})`:""}`)}const l=await r.text();return n.addSequence({sequence:l,start:a,stop:o}),l}async getRefNameAliases(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),l=new URLSearchParams({assembly:e});o.search=l.toString();const s=o.toString(),i=await this.fetch(n,s);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),l=new URLSearchParams({assembly:e});o.search=l.toString();const s=o.toString(),i=await this.fetch(n,s);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 n=a.getConf(t,["sequence","metadata"]);return!(!(n&&n.apollo&&n.internetAccountConfigId)||e&&n.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,l=new URL("changes",r).href,s=await this.fetch(o,l,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!s.ok){const e=await Dt(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class Ur extends Or{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 l=r.refSeqs.get(a);return l?{seq:l.getSequence(o,n),refSeq:a}:{seq:"",refSeq:a}}async getRefNameAliases(e){const t=this.clientStore.assemblies.get(e),n=[];if(!t)return n;for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getRegions(e){const t=this.clientStore.assemblies.get(e);if(!t)return[];const n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){const{clientStore:a}=this,{assemblies:o}=a;a.clearCheckResults();for(const[,e]of o)if("InMemoryFileDriver"===e.backendDriverType){const t=await ft(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class $r extends Or{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:o}=a.getConf(n,["sequence","metadata"]),l=require("node:fs");return dt(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=(await this.getAssembly(t)).refSeqs.get(a);if(!r)throw new Error(`refSeq ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(n){if(!e.isAssemblySpecificChange(n))throw new Error(`Cannot use this type of change with local file: "${n.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),l=o.get(n.assembly);if(!l)throw new Error(`Could not find assembly with name "${n.assembly}"`);const{file:s}=a.getConf(l,["sequence","metadata"]),i=this.clientStore.assemblies.get(n.assembly);if(!i)throw new Error(`Could not find assembly in client with name "${n.assembly}"`);const u=new Set(...i.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await ft(i);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of i.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of i.comments)m.push({comment:e});for(const[,e]of i.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(c.getSnapshot(e)))}for(const[,e]of i.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=Ne.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function jr(e,n){const o=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",X.AnnotationFeatureModel),l=function(e){return c.types.model("ClientDataStore",{typeName:c.types.optional(c.types.literal("Client"),"Client"),assemblies:c.types.map(X.ApolloAssembly),checkResults:c.types.map(X.CheckResult),ontologyManager:c.types.optional(on,{})}).views((t=>({get internetAccounts(){return c.getRoot(t).internetAccounts},get pluginConfiguration(){return c.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>c.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):c.getParentOfType(n,X.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new _r(e),collaborationServerDriver:new Br(e),inMemoryFileDriver:new Ur(e),desktopFileDriver:r.isElectron?new $r(e):void 0}))).actions((e=>({afterCreate(){c.addDisposer(e,i.autorun((()=>{const{ontologyManager:t,pluginConfiguration:n}=e,o=n.ontologies;for(const n of o||[]){const[o,l,s,i]=[a.readConfObject(n,"name"),a.readConfObject(n,"version"),a.readConfObject(n,"source"),a.readConfObject(n,"textIndexFields")];if(!t.findOntology(o)){const n=r.getSession(e),{jobsManager:a}=n,c=new AbortController,u=`Loading ontology "${o}"`,d={name:u,statusMessage:`Loading ontology "${o}", version "${l}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(),a.abortJob(d.name)}};t.addOntology(o,l,s,{textIndexing:{indexFields:i},update:(e,t)=>{0!==t?100!==t?a.update(u,e,t):a.done(d):a.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){if(!t)return e.collaborationServerDriver;const n=r.getSession(e),{assemblyManager:o}=n,l=o.get(t);if(!l)return e.collaborationServerDriver;const{file:s,internetAccountConfigId:i}=a.getConf(l,["sequence","metadata"]);return r.isElectron&&s?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,n){if(!(t??n))throw new Error("Must provide either assemblyName or internetAccountId");let o=n;if(t&&!o){const{assemblyManager:n}=r.getSession(e),l=n.get(t);if(!l)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=a.getConf(l,["sequence","metadata"]))}const{internetAccounts:l}=e,s=l.find((e=>e.internetAccountId===o));if(!s)throw new Error(`No InternetAccount found with config id ${n}`);return s}}))).actions((e=>({loadFeatures:c.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:l}=n;let s=e.assemblies.get(r);s||(s=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=s.refSeqs.get(i.refSeq);c||(c=s.refSeqs.put({_id:i.refSeq,name:l,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:c.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:l,refName:s,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:s,sequence:[]})),u.addSequence({start:i,stop:l,sequence:o})}}))})))}(o),s=n.props({apolloDataStore:c.types.optional(l,{typeName:"Client"}),apolloSelectedFeature:c.types.safeReference(o),jobsManager:c.types.optional(Pr,{}),isLocked:c.types.optional(c.types.boolean,!1)}).volatile((()=>({apolloHoveredFeature:void 0,abortController:new AbortController}))).extend((()=>{const e=i.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},apolloSetHoveredFeature(t){e.apolloHoveredFeature=t},addApolloTrackConfig(t,n){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${a.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...n?{baseURL:{uri:n,locationType:"UriLocation"}}:{}}}})},toggleLocked(){e.isLocked=!e.isLocked},getPluginConfiguration(){const{jbrowse:t}=c.getRoot(e);return t.configuration.ApolloPlugin},broadcastLocations(){const{internetAccounts:t}=c.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).volatile((e=>({previousSnapshot:c.getSnapshot(e)}))).actions((e=>({afterCreate(){c.applySnapshot(e,{name:e.name,id:e.id});const{internetAccounts:t,jbrowse:n,reloadPluginManagerCallback:o}=c.getRoot(e);c.addDisposer(e,i.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}),{name:"ApolloSessionBroadcastLocations"})),c.addDisposer(e,i.autorun((async r=>{if(a.readConfObject(n.configuration.ApolloPlugin,"hasRole"))return c.applySnapshot(e,e.previousSnapshot),void r.dispose();const{signal:l}=e.abortController;for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t}=n,a=new URL("jbrowse/config.json",t).href,s=n.getFetcher({locationType:"UriLocation",uri:a});let i,c;try{i=await s(a,{signal:l})}catch(t){e.abortController.signal.aborted||console.error(t);continue}if(i.ok){try{c=await i.json()}catch(e){console.error(e);continue}o(c,e.previousSnapshot),r.dispose()}else{const e=await Dt(i,"Failed to fetch assemblies");console.error(e)}}}),{name:"ApolloSessionLoadConfig"}))},beforeDestroy(){e.abortController.abort("destroying session model")}}))).views((e=>{const n=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return n?.(o);const r=a.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...n?.(o)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=c.getRoot(e),l=c.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const i={...c.getSnapshot(o),trackId:r.slice(0,r.length-13)};for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:s?.tracks&&[...s.tracks,i]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(i)},icon:ct.default}]:[...n?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=c.getRoot(e),l=c.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const i=s?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:i}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:ct.default}]}}}));return c.types.snapshotProcessor(s,{postProcessor(e,t){e.apolloSelectedFeature=void 0;const n=Object.fromEntries(Object.entries(e.apolloDataStore.assemblies).filter((([,e])=>"InMemoryFileDriver"===e.backendDriverType)));if(e.apolloDataStore={typeName:"Client",assemblies:n,checkResults:{}},!t)return e;const{apolloDataStore:a}=t,{checkResults:o}=a;for(const[,t]of o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=c.getSnapshot(t))}return e}})}const Gr="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Wr=new t.CDSCheck;e.checkRegistry.registerCheck(Wr.name,Wr);const zr=new t.TranscriptCheck;e.checkRegistry.registerCheck(zr.name,zr),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends ye.default{name="ApolloPlugin";version="0.3.8";configurationSchema=pr;install(e){!function(e){e.addAdapterType((()=>new _e.default({name:"ApolloSequenceAdapter",configSchema:ea,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Qn})))}(e),function(e){e.addAdapterType((()=>new _e.default({name:"ApolloRefNameAliasAdapter",configSchema:Kn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Xn})))}(e),function(e){e.addTextSearchAdapterType((()=>new o.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:na,AdapterClass:ta,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new o.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:wa,ReactComponent:Sa})})),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloTranscriptDetails",{});return new o.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:Ea,ReactComponent:Pa})})),e.addTrackType((()=>{const t=a.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:o.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new o.TrackType({name:"ApolloTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new o.InternetAccountType({name:"ApolloInternetAccount",configSchema:ut,stateModel:Vn(ut)}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloDisplay",configSchema:Oa,stateModel:Jo(0,Oa),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Lr}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:or,stateModel:gr(0,or),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:qr}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:Xo,stateModel:nr(0,Xo),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:ar}))),e.addToExtensionPoint("Core-extendSession",jr.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:be.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[pn,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Cr),e.addToExtensionPoint("Core-extendPluggableElement",Ar),Gr||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:l}=n;switch(l){case"getSequence":{const{region:a}=n,{assemblyName:l}=a,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const i=s.getBackendDriver(l),{seq:c}=await i.getSequence(a);t.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a),i=await s.getRegions(a);t.workers[0].postMessage({apollo:o,messageId:r,regions:i});break}case"getRefNameAliases":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a),i=await s.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){var t;r.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("colorFeature",(e=>{if("pseudogenic_transcript"===e)return s.alpha("rgb(148, 203, 236)",.6);if("nonCodingTranscript"===e)return s.alpha("rgb(194, 106, 119)",.6);throw new Error("Invalid type")})),(t=e.rootModel).insertInMenu("Apollo",{label:"Redo",icon:lt.default,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),t.insertInMenu("Apollo",{label:"Undo",icon:it.default,onClick(e){const{apolloDataStore:t}=e;t.changeManager.undoLastChange()}},0),t.appendToMenu("Apollo",{label:"Download GFF3",icon:nt.default,onClick:e=>{e.queueDialog((t=>[wn,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"View Change Log",icon:st.default,onClick:e=>{e.queueDialog((t=>[Rn,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Open local GFF3 file",icon:ot.default,onClick:e=>{e.queueDialog((t=>[Dn,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),t.appendToMenu("Apollo",{label:"View check results",icon:at.default,onClick:e=>{e.queueDialog((t=>[qn,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Lock/Unlock session",onClick:e=>{e.toggleLocked()}}),t.appendToMenu("Apollo",{label:"Log out",icon:rt.default,onClick:e=>{e.queueDialog((t=>[Cn,{session:e,handleClose:()=>{t()}}]))}}))}};
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