Mercurial > repos > fubar > jbrowse2

comparison x/static/js/6837.a706c464.chunk.js @ 125:49f3d3878413 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
author fubar
date Sat, 05 Oct 2024 23:58:05 +0000
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124:137e08517410 125:49f3d3878413
1 (globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[6837],{9342:(e,t,r)=>{"use strict";r.d(t,{Q:()=>a,n:()=>m});var n=r(68584);const a=(0,n.ConfigurationSchema)("BaseFeatureWidget",{});var o=r(36422),i=r(42489),s=r(33039),l=r.n(s),c=r(99546),d=r(8832);function u(e,t){return+((0,c.localStorageGetItem)(e)??t)}function p(e,t,r,n=0,a={}){t<=n||e.subfeatures?.map((e=>{p(e,t,r,n+1,a),r(e)}))}function m(e){return 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extends p.A{name="CoreFreeResources";async execute(e){let t=0;return t+=(0,C.pZ)(e),this.pluginManager.getRendererTypes().forEach((e=>{const r=e.freeResources();r&&(t+=r)})),t}async serializeArguments(e,t){return e}}class D extends p.A{name="CoreGetFeatureDensityStats";async serializeArguments(e,t){const{rootModel:r}=this.pluginManager,n=r.session.assemblyManager,a=await(0,T.renameRegionsIfNeeded)(n,{...e,filters:e.filters?.toJSON().filters});return super.serializeArguments(a,t)}async execute(e,t){const r=this.pluginManager,n=await this.deserializeArguments(e,t),{adapterConfig:a,sessionId:o,regions:i}=n,{dataAdapter:s}=await(0,C.cK)(r,o,a);if(!(0,S.isFeatureAdapter)(s))throw new Error("Adapter does not support retrieving features");return s.getMultiRegionFeatureDensityStats(i,n)}}var B=r(58921);const V=(0,f.ConfigurationSchema)("CytobandAdapter",{cytobandLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/cytoband.txt.gz"}}},{explicitlyTyped:!0});class z extends 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l.types.compose("LinearReadArcsDisplay",Q.BaseDisplay,(0,D._e)(),(0,D.e6)(),l.types.model({type:l.types.literal("LinearReadArcsDisplay"),configuration:(0,o.ConfigurationReference)(e),filterBy:l.types.optional(U.O2,{}),lineWidth:l.types.maybe(l.types.number),jitter:l.types.maybe(l.types.number),colorBy:l.types.maybe(l.types.model({type:l.types.string,tag:l.types.maybe(l.types.string),extra:l.types.frozen()})),drawInter:!0,drawLongRange:!0})).volatile((()=>({loading:!1,chainData:void 0,lastDrawnOffsetPx:void 0,lastDrawnBpPerPx:0,ref:null}))).actions((e=>({setLastDrawnOffsetPx(t){e.lastDrawnOffsetPx=t},setLastDrawnBpPerPx(t){e.lastDrawnBpPerPx=t},setLoading(t){e.loading=t},reload(){e.error=void 0},setRef(t){e.ref=t},setColorScheme(t){e.colorBy=(0,l.cast)(t)},setChainData(t){e.chainData=t},setDrawInter(t){e.drawInter=t},setDrawLongRange(t){e.drawLongRange=t},setFilterBy(t){e.filterBy=(0,l.cast)(t)},setLineWidth(t){e.lineWidth=t},setJitter(t){e.jitter=t}}))).views((e=>({get drawn(){return 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ne(e){e.addDisplayType((()=>{const t=function(e){return(0,o.ConfigurationSchema)("LinearReadArcsDisplay",{maxFeatureScreenDensity:{type:"number",description:"maximum features per pixel that is displayed in the view",defaultValue:5},lineWidth:{type:"number",description:"set arc line width",defaultValue:1},jitter:{type:"number",description:"jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them",defaultValue:0},colorScheme:{type:"stringEnum",model:l.types.enumeration("colorScheme",["strand","normal","insertSize","insertSizeAndOrientation","mappingQuality","tag"]),description:"color scheme to use",defaultValue:"normal"}},{baseConfiguration:(0,D.lw)(e),explicitlyTyped:!0})}(e);return new L.A({name:"LinearReadArcsDisplay",displayName:"Arc 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renderSvg(t){const{renderSvg:n}=await r.e(9028).then(r.bind(r,59028)),{drawFeats:a}=await r.e(6946).then(r.bind(r,26946));return n(e,t,a)}}})).actions((e=>({afterAttach(){(async()=>{try{const{doAfterAttach:t}=await r.e(9070).then(r.bind(r,9070)),{drawFeats:n}=await r.e(6946).then(r.bind(r,26946));t(e,n)}catch(t){console.error(t),e.setError(t)}})()}})))};function ie(e){e.addDisplayType((()=>{const t=function(e){return(0,o.ConfigurationSchema)("LinearReadCloudDisplay",{maxFeatureScreenDensity:{type:"number",description:"maximum features per pixel that is displayed in the view",defaultValue:5},featureHeight:{type:"number",defaultValue:7},colorScheme:{type:"stringEnum",model:l.types.enumeration("colorScheme",["strand","normal","insertSize","insertSizeAndOrientation","mappingQuality","tag"]),description:"color scheme to use",defaultValue:"normal"}},{baseConfiguration:(0,D.lw)(e),explicitlyTyped:!0})}(e);return new L.A({name:"LinearReadCloudDisplay",displayName:"Read cloud 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this.deserializeArguments(e,t),{adapterConfig:n,sessionId:a,regions:o}=r,i=(await(0,S.cK)(this.pluginManager,a,n)).dataAdapter,s=await(0,he._)(i.getFeaturesInMultipleRegions(o,r).pipe((0,ge.$)())),l=(0,y.dedupe)(s.map((e=>({id:e.id(),refName:e.get("refName"),name:e.get("name"),start:e.get("start"),strand:e.get("strand"),end:e.get("end"),flags:e.get("flags"),tlen:e.get("template_length"),pair_orientation:e.get("pair_orientation"),next_ref:e.get("next_ref"),next_pos:e.get("next_pos"),clipPos:e.get("clipPos"),SA:(0,A.bH)(e,"SA")}))),(e=>e.id)),c=l.filter((e=>2&e.flags&&!(256&e.flags)&&!(2048&e.flags))),d=c.length?function(e){const t=e.map((e=>Math.abs(e.tlen))),r=t.reduce(((e,t)=>e+t),0),n=t.map((e=>e*e)).reduce(((e,t)=>e+t),0),a=t.length,o=r/a,i=Math.sqrt((a*n-r*r)/(a*a));return{upper:o+4*i,lower:o-3*i,avg:o,sd:i}}(c):void 0,u=(0,y.groupBy)(l,(e=>e.name));return{chains:Object.values(u),stats:d,hasPaired:!!d,containsNoTransferables:!0}}}var we=r(80544);class ve extends ye{name="PileupGetVisibleModifications";async execute(e,t){const{adapterConfig:r,sessionId:n,regions:a}=await this.deserializeArguments(e,t),o=(await(0,S.cK)(this.pluginManager,n,r)).dataAdapter,i=await(0,he._)(o.getFeaturesInMultipleRegions(a).pipe((0,ge.$)())),s=new Set;return i.forEach((e=>{(0,we.getModificationTypes)((0,A.c$)(e,"MM","Mm")||"").forEach((e=>s.add(e)))})),[...s]}}class Ce extends ye{name="PileupGetGlobalValueForTag";async execute(e,t){const{adapterConfig:r,sessionId:n,regions:a,tag:o}=await this.deserializeArguments(e,t),i=(await(0,S.cK)(this.pluginManager,n,r)).dataAdapter.getFeaturesInMultipleRegions(a),s=await(0,he._)(i.pipe((0,ge.$)()));return[...new Set(s.map((e=>(0,A.bH)(e,o))).filter((e=>void 0!==e)).map((e=>`${e}`)))]}}function Se(e){e.addRpcMethod((()=>new Ce(e))),e.addRpcMethod((()=>new ve(e))),e.addRpcMethod((()=>new be(e)))}var ke=r(91468);function Te(e){e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const 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l.types.compose(D.Lr,l.types.model({configuration:(0,o.ConfigurationReference)(e),featureHeight:l.types.maybe(l.types.number),noSpacing:l.types.maybe(l.types.boolean),fadeLikelihood:l.types.maybe(l.types.boolean),trackMaxHeight:l.types.maybe(l.types.number),colorBy:Ve.Qg,filterBy:l.types.optional(U.O2,{}),jexlFilters:l.types.optional(l.types.array(l.types.string),[])})).volatile((()=>({colorTagMap:B.observable.map({}),featureUnderMouseVolatile:void 0,tagsReady:!1}))).views((e=>({get autorunReady(){return(0,y.getContainingView)(e).initialized&&e.featureDensityStatsReady&&!e.regionTooLarge}}))).actions((e=>({setTagsReady(t){e.tagsReady=t},setMaxHeight(t){e.trackMaxHeight=t},setFeatureHeight(t){e.featureHeight=t},setNoSpacing(t){e.noSpacing=t},setColorScheme(t){e.colorTagMap=B.observable.map({}),e.colorBy=(0,l.cast)(t),t.tag&&(e.tagsReady=!1)},updateColorTagMap(t){const r=["#BBCCEE","pink","#CCDDAA","#EEEEBB","#FFCCCC","lightblue","lightgreen","tan","#CCEEFF","lightsalmon"];t.forEach((t=>{if(!e.colorTagMap.has(t)){const n=[...e.colorTagMap.keys()].length;e.colorTagMap.set(t,r[n])}}))},setFeatureUnderMouse(t){e.featureUnderMouseVolatile=t},selectFeature(t){const r=(0,y.getSession)(e);if((0,y.isSessionModelWithWidgets)(r)){const n=r.addWidget("AlignmentsFeatureWidget","alignmentFeature",{featureData:t.toJSON(),view:(0,y.getContainingView)(e),track:(0,y.getContainingTrack)(e)});r.showWidget(n)}r.setSelection(t)},copyFeatureToClipboard(t){const{uniqueId:r,...n}=t.toJSON(),a=(0,y.getSession)(e);Ie()(JSON.stringify(n,null,4)),a.notify("Copied to clipboard","success")},setConfig(t){e.configuration=t},setFilterBy(t){e.filterBy=(0,l.cast)(t)},setJexlFilters(t){e.jexlFilters=(0,l.cast)(t)}}))).views((e=>({get rendererConfig(){const{featureHeight:t,noSpacing:r,trackMaxHeight:n,rendererTypeName:a}=e,i=(0,o.getConf)(e,["renderers",a])||{};return 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a.setVolatileWidth(e.width),a.moveTo(t,r),a.dynamicBlocks.contentBlocks.map((e=>({...e,start:Math.floor(e.start),end:Math.ceil(e.end)})))},afterDisplayedRegionsSet(t){e.afterDisplayedRegionsSetCallbacks.push(t)},horizontalScroll(t){const r=e.offsetPx;return e.scrollTo(e.offsetPx+t)-r},center(){const t=e.totalBp/2/e.bpPerPx;e.scrollTo(Math.round(t-e.width/2))},showAllRegions(){e.zoomTo(e.maxBpPerPx),this.center()},showAllRegionsInAssembly(t){const r=(0,a.getSession)(e),{assemblyManager:n}=r;if(!t){const n=new Set(e.displayedRegions.map((e=>e.assemblyName)));if(n.size>1)return void r.notify("Can't perform operation with multiple assemblies currently");[t]=[...n]}const o=n.get(t);if(o){const{regions:t}=o;t&&(this.setDisplayedRegions(t),e.zoomTo(e.maxBpPerPx),this.center())}},setDraggingTrackId(t){e.draggingTrackId=t},setScaleFactor(t){e.scaleFactor=t},clearView(){this.setDisplayedRegions([]),e.tracks.clear(),e.scrollTo(0),e.zoomTo(10)},async exportSvg(t={}){const{renderToSvg:n}=await Promise.resolve().then(r.bind(r,98753)),a=await n(e,t),o=new Blob([a],{type:"image/svg+xml"});(0,_.saveAs)(o,t.filename||"image.svg")}}))).actions((e=>{let t=()=>{};return{slide:function(r){const[n,o]=(0,a.springAnimate)(e.offsetPx,e.offsetPx+e.width*r,e.scrollTo,void 0,void 0,200);t(),t=o,n()}}})).actions((e=>{let t=()=>{};return{zoom:function(r){if(e.zoomTo(e.bpPerPx),r<e.bpPerPx&&e.bpPerPx===e.minBpPerPx||r>e.bpPerPx&&e.bpPerPx===e.maxBpPerPx)return;const n=e.bpPerPx/r,[o,i]=(0,a.springAnimate)(1,n,e.setScaleFactor,(()=>{e.zoomTo(r),e.setScaleFactor(1)}));t(),t=i,o()}}})).views((e=>({get canShowCytobands(){return 1===e.displayedRegions.length&&this.anyCytobandsExist},get showCytobands(){return this.canShowCytobands&&e.showCytobandsSetting},get anyCytobandsExist(){const{assemblyManager:t}=(0,a.getSession)(e);return e.assemblyNames.some((e=>t.get(e)?.cytobands?.length))},get cytobandOffset(){return 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ct(e.coarseDynamicBlocks)}}})).actions((e=>({setCoarseDynamicBlocks(t){e.coarseDynamicBlocks=t.contentBlocks,e.coarseTotalBp=t.totalBp},afterAttach(){(0,i.addDisposer)(e,(0,m.autorun)((()=>{e.initialized&&this.setCoarseDynamicBlocks(e.dynamicBlocks)}),{delay:150})),(0,i.addDisposer)(e,(0,m.autorun)((()=>{const t=e=>JSON.stringify(e),{showCytobandsSetting:r,showCenterLine:n,colorByCDS:o}=e;(0,a.localStorageSetItem)("lgv-showCytobands",t(r)),(0,a.localStorageSetItem)("lgv-showCenterLine",t(n)),(0,a.localStorageSetItem)("lgv-colorByCDS",t(o))})))}}))).actions((e=>({moveTo(t,r){(0,q.tw)(e,t,r)},async navToLocString(t,r){const{assemblyNames:n}=e,{assemblyManager:o}=(0,a.getSession)(e),i=r||n[0];return i&&await o.waitForAssembly(i),this.navToLocations((0,Re.CU)(t,i,((e,t)=>o.isValidRefName(e,t))),i)},async navToSearchString({input:t,assembly:r}){await(0,qe.cm)({input:t,assembly:r,model:e})},async navToLocations(t,r){const{assemblyManager:n}=(0,a.getSession)(e);await(0,m.when)((()=>void 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"${d}"`);const m=void 0===r.start?u.start:r.start,g=void 0===r.end?u.end:r.end,h=void 0===n.start?p.start:n.start,f=void 0===n.end?p.end:n.end,y=e.displayedRegions.findIndex((e=>c===e.refName&&m>=e.start&&m<=e.end&&g<=e.end&&g>=e.start)),b=e.displayedRegions.findIndex((e=>d===e.refName&&h>=e.start&&h<=e.end&&f<=e.end&&f>=e.start));if(-1===y||-1===b)throw new Error(`could not find a region that contained "${t.map((e=>(0,a.assembleLocString)(e)))}"`);const w=e.displayedRegions[y],v=e.displayedRegions[b];this.moveTo({index:y,offset:w.reversed?w.end-g:m-w.start},{index:b,offset:v.reversed?v.end-h:f-v.start})}}))).views((e=>({rubberBandMenuItems:()=>[{label:"Zoom to region",icon:te.A,onClick:()=>{e.moveTo(e.leftOffset,e.rightOffset)}},{label:"Get sequence",icon:g.A,onClick:()=>{(0,a.getSession)(e).queueDialog((t=>[st,{model:e,handleClose:t}]))}}],bpToPx:({refName:t,coord:r,regionNumber:n})=>(0,q.eB)({refName:t,coord:r,regionNumber:n,self:e}),centerAt(t,r,n){const a=this.bpToPx({refName:r,coord:t,regionNumber:n});void 0!==a&&e.scrollTo(Math.round(a.offsetPx-e.width/2))},pxToBp:t=>(0,q.Ii)(e,t),get centerLineInfo(){return e.displayedRegions.length>0?this.pxToBp(e.width/2):void 0}}))).actions((e=>({afterCreate(){function t(t){(0,a.getSession)(e).focusedViewId===e.id&&(t.ctrlKey||t.metaKey)&&("ArrowLeft"===t.code?(t.preventDefault(),e.slide(-.9)):"ArrowRight"===t.code?(t.preventDefault(),e.slide(.9)):"ArrowUp"===t.code&&1===e.scaleFactor?(t.preventDefault(),e.zoom(e.bpPerPx/2)):"ArrowDown"===t.code&&1===e.scaleFactor&&(t.preventDefault(),e.zoom(2*e.bpPerPx)))}document.addEventListener("keydown",t),(0,i.addDisposer)(e,(()=>{document.removeEventListener("keydown",t)}))}}))).preProcessSnapshot((e=>{if(!e)return e;const{highlight:t,...r}=e;return{highlight:Array.isArray(t)||void 0===t?t:[t],...r}}))}const ut=function(e){return(0,o.ConfigurationSchema)("LinearBasicDisplay",{renderer:e.pluggableConfigSchemaType("renderer")},{baseConfiguration:l,explicitlyTyped:!0})};var pt=r(93100);const mt=(0,c.lazy)((()=>r.e(4033).then(r.bind(r,34033)))),gt=(0,c.lazy)((()=>r.e(2412).then(r.bind(r,92412)))),ht=function(e){return i.types.compose("LinearBasicDisplay",x,i.types.model({type:i.types.literal("LinearBasicDisplay"),trackShowLabels:i.types.maybe(i.types.boolean),trackShowDescriptions:i.types.maybe(i.types.boolean),trackDisplayMode:i.types.maybe(i.types.string),trackMaxHeight:i.types.maybe(i.types.number),configuration:(0,o.ConfigurationReference)(e),jexlFilters:i.types.maybe(i.types.array(i.types.string))})).views((e=>({get activeFilters(){return e.jexlFilters??(0,o.getConf)(e,"jexlFilters").map((e=>`jexl:${e}`))},get rendererTypeName(){return(0,o.getConf)(e,["renderer","type"])},get showLabels(){return e.trackShowLabels??(0,o.getConf)(e,["renderer","showLabels"])},get showDescriptions(){return e.trackShowDescriptions??(0,o.getConf)(e,["renderer","showDescriptions"])},get maxHeight(){return e.trackMaxHeight??(0,o.getConf)(e,["renderer","maxHeight"])},get displayMode(){return e.trackDisplayMode??(0,o.getConf)(e,["renderer","displayMode"])}}))).views((e=>({get rendererConfig(){const t=(0,o.getConf)(e,["renderer"])||{};return e.rendererType.configSchema.create({...t,showLabels:e.showLabels,showDescriptions:e.showDescriptions,displayMode:e.displayMode,maxHeight:e.maxHeight},(0,i.getEnv)(e))}}))).actions((e=>({setJexlFilters(t){e.jexlFilters=(0,i.cast)(t)},toggleShowLabels(){e.trackShowLabels=!e.showLabels},toggleShowDescriptions(){e.trackShowDescriptions=!e.showDescriptions},setDisplayMode(t){e.trackDisplayMode=t},setMaxHeight(t){e.trackMaxHeight=t}}))).views((e=>{const{trackMenuItems:t,renderProps:r}=e;return{renderProps:()=>({...r(),config:e.rendererConfig,filters:new pt.A({filters:e.activeFilters})}),trackMenuItems:()=>[...t(),{label:"Show labels",icon:K.A,type:"checkbox",checked:e.showLabels,onClick:()=>{e.toggleShowLabels()}},{label:"Show descriptions",icon:K.A,type:"checkbox",checked:e.showDescriptions,onClick:()=>{e.toggleShowDescriptions()}},{label:"Display mode",icon:K.A,subMenu:["compact","reducedRepresentation","normal","collapse"].map((t=>({label:t,onClick:()=>{e.setDisplayMode(t)}})))},{label:"Set max height",onClick:()=>{(0,a.getSession)(e).queueDialog((t=>[mt,{model:e,handleClose:t}]))}},{label:"Edit filters",onClick:()=>{(0,a.getSession)(e).queueDialog((t=>[gt,{model:e,handleClose:t}]))}}]}}))};var ft=r(26612);class yt extends n.A{name="LinearGenomeViewPlugin";exports={BaseLinearDisplayComponent:V,BaseLinearDisplay:x,baseLinearDisplayConfigSchema:l,SearchBox:Je,ZoomControls:Ge,LinearGenomeView:rt.default};configurationSchema=(0,o.ConfigurationSchema)("LinearGenomeViewConfigSchema",{trackLabels:{type:"string",defaultValue:"overlapping",model:i.types.enumeration("trackLabelOptions",["offset","overlapping","hidden"])}});install(e){var t;(t=e).addTrackType((()=>{const e=(e=>(0,o.ConfigurationSchema)("FeatureTrack",{},{baseConfiguration:(0,z.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}))(t);return new z.TrackType({name:"FeatureTrack",displayName:"Feature track",configSchema:e,stateModel:(0,z.createBaseTrackModel)(t,"FeatureTrack",e)})})),function(e){e.addTrackType((()=>{const t=(e=>(0,o.ConfigurationSchema)("BasicTrack",{},{baseConfiguration:(0,z.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}))(e);return new z.TrackType({name:"BasicTrack",configSchema:t,stateModel:(0,z.createBaseTrackModel)(e,"BasicTrack",t)})}))}(e),function(e){e.addDisplayType((()=>{const t=ut(e);return new z.DisplayType({name:"LinearBasicDisplay",displayName:"Basic feature display",configSchema:t,stateModel:ht(t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:V})}))}(e),function(e){e.addViewType((()=>new z.ViewType({name:"LinearGenomeView",displayName:"Linear genome view",stateModel:dt(e),ReactComponent:(0,c.lazy)((()=>Promise.resolve().then(r.bind(r,98273))))})))}(e),function(e){e.addDisplayType((()=>{const t=O(e);return new z.DisplayType({name:"LinearBareDisplay",configSchema:t,displayName:"Bare feature display",stateModel:H(t),trackType:"BasicTrack",viewType:"LinearGenomeView",ReactComponent:V})}))}(e),function(e){e.addToExtensionPoint("LaunchView-LinearGenomeView",(async({session:e,assembly:t,loc:r,tracks:n=[],tracklist:o,nav:i,highlight:s})=>{try{const{assemblyManager:l}=e,{isValidRefName:c}=l,d=e.addView("LinearGenomeView",{});if(await(0,a.when)((()=>!!d.volatileWidth)),!t)throw new Error("No assembly provided when launching linear genome view");const u=await l.waitForAssembly(t);if(!u)throw new Error(`Assembly "${t}" not found when launching linear genome view`);o&&d.activateTrackSelector(),void 0!==i&&d.setHideHeader(!i),void 0!==s&&s.forEach((async e=>{const r=(0,a.parseLocString)(e,(e=>c(e,t))),{start:n,end:o}=r;void 0!==n&&void 0!==o&&d.addToHighlights({...r,start:n,end:o,assemblyName:t})})),await(0,qe.cm)({input:r,model:d,assembly:u});const p=[];if(n.forEach((e=>{!function(e,t,r){try{e.showTrack(t)}catch(e){if(!/Could not resolve identifier/.exec(`${e}`))throw e;r.push(t)}}(d,e,p)})),p.length)throw new Error(`Could not resolve identifiers: ${p.join(",")}`)}catch(t){throw e.notifyError(`${t}`,t),t}}))}(e)}configure(e){(0,a.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Linear genome view",icon:s.A,onClick:e=>{e.addView("LinearGenomeView",{})}})}}},6184:(e,t,r)=>{"use strict";r.d(t,{Kd:()=>o,cm:()=>i});var n=r(99546),a=r(8656);async function o({option:e,model:t,assemblyName:r}){const n=e.getLocation(),a=e.getTrackId();n&&(await t.navToLocString(n,r),a&&t.showTrack(a))}async function i({input:e,model:t,assembly:r}){const i=r.allRefNamesWithLowerCase||[],s=r.name;if(e.split(" ").every((e=>function(e,t){const[r,n]=function(e){const t=e.lastIndexOf(":");if(-1===t)return[e,""];return[e.slice(0,t),e.slice(t+1)]}(e);return t.includes(e)||t.includes(r)&&!Number.isNaN(Number.parseInt(n,10))}(e,i))))await t.navToLocString(e,r.name);else{const i=t.searchScope(s),{textSearchManager:l}=(0,n.getSession)(t),c=await async function({queryString:e,searchType:t,searchScope:r,rankSearchResults:o,textSearchManager:i,assembly:s}){i||console.warn("No text search manager");const l=await(i?.search({queryString:e,searchType:t},r,o)),c=s?.allRefNames?.filter((t=>t.toLowerCase().startsWith(e.toLowerCase()))).slice(0,10).map((e=>new a.A({label:e})));return(0,n.dedupe)([...c||[],...l||[]],(e=>e.getId()))}({queryString:e,searchType:"exact",searchScope:i,rankSearchResults:t.rankSearchResults,textSearchManager:l,assembly:r});c.length>1?t.setSearchResults(c,e.toLowerCase(),s):1===c.length?await o({option:c[0],model:t,assemblyName:s}):await t.navToLocString(e,s)}}},54702:(e,t,r)=>{"use strict";r.d(t,{A:()=>l});var n=r(9502);const a={DEL:"deletion",INS:"insertion",DUP:"duplication",INV:"inversion",INVDUP:"inverted_duplication",CNV:"copy_number_variation",TRA:"translocation","DUP:TANDEM":"tandem_duplication",NON_REF:"sequence_variant","*":"sequence_variant"};function o(e,t,r){if(!t||0===t.length)return["remark","no alternative alleles"];const a=new Set;let o=new Set;if(t.forEach((t=>{let[l,c]=i(t,r);l||([l,c]=function(e,t){if((0,n.h)(t))return["breakend",t];if(1===e.length&&1===t.length)return["SNV",s("SNV",e,t)];if("<INS>"===t)return["insertion",t];if("<DEL>"===t)return["deletion",t];if("<DUP>"===t)return["duplication",t];if("<CNV>"===t)return["cnv",t];if("<INV>"===t)return["inversion",t];if("<TRA>"===t)return["translocation",t];if(t.includes("<"))return["sv",t];if(e.length===t.length)return e.split("").reverse().join("")===t?["inversion",s("inversion",e,t)]:["substitution",s("substitution",e,t)];if(e.length<=t.length){const r=t.length-e.length,n=r.toLocaleString("en-US");return["insertion",r>5?`${n}bp INS`:s("insertion",e,t)]}if(e.length>t.length){const r=e.length-t.length,n=r.toLocaleString("en-US");return["deletion",r>5?`${n}bp DEL`:s("deletion",e,t)]}return["indel",s("indel",e,t)]}(e,t)),l&&c&&(a.add(l),o.add(c))})),o.size>1){const e=[...o],t=new Set(e.map((e=>{const t=e.split("->");return 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F extends s{async draw(e,t){const{config:r}=t,n=(0,c.readConfObject)(r,"color");return N(e,{...t,offset:y.YSCALEBAR_LABEL_OFFSET,colorCallback:"#f0f"===n?()=>"grey":e=>(0,c.readConfObject)(r,"color",{feature:e})})}}var L=r(56328),D=r(20529);function B(){return(0,c.ConfigurationSchema)("SharedWiggleDisplay",{autoscale:{type:"stringEnum",defaultValue:"local",model:g.types.enumeration("Autoscale type",["global","local","globalsd","localsd","zscore"]),description:"global/local using their min/max values or w/ standard deviations (globalsd/localsd)"},minimalTicks:{type:"boolean",defaultValue:!1,description:"use the minimal amount of ticks"},minScore:{type:"number",defaultValue:Number.MIN_VALUE,description:"minimum value for the y-scale"},maxScore:{type:"number",description:"maximum value for the y-scale",defaultValue:Number.MAX_VALUE},numStdDev:{type:"number",description:"number of standard deviations to use for autoscale types globalsd or 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0}))).actions((e=>({updateQuantitativeStats(t){const{scoreMin:r,scoreMax:n}=t,a=1e-6;e.stats?(Math.abs(e.stats.scoreMax-n)>a||Math.abs(e.stats.scoreMin-r)>a)&&(e.stats={scoreMin:r,scoreMax:n}):e.stats={scoreMin:r,scoreMax:n}},setColor(t){e.color=t},setPosColor(t){e.posColor=t},setNegColor(t){e.negColor=t},setLoading(t){const{statsFetchInProgress:r}=e;void 0===r||r.signal.aborted||r.abort(),e.statsFetchInProgress=t},selectFeature(t){const r=(0,i.getSession)(e);(0,i.isSelectionContainer)(r)&&r.setSelection(t)},setResolution(t){e.resolution=t},setFill(t){0===t?(e.fill=!0,e.minSize=0):1===t?(e.fill=!1,e.minSize=1):2===t&&(e.fill=!1,e.minSize=2)},toggleLogScale(){e.scale="log"===e.scale?"linear":"log"},setScaleType(t){e.scale=t},setSummaryScoreMode(t){e.summaryScoreMode=t},setAutoscale(t){e.autoscale=t},setMaxScore(t){e.constraints.max=t},setRendererType(t){e.rendererTypeNameState=t},setMinScore(t){e.constraints.min=t},toggleCrossHatches(){e.displayCrossHatches=!e.displayCrossHatches},setCrossHatches(t){e.displayCrossHatches=t}}))).views((e=>({get adapterTypeName(){return e.adapterConfig.type},get rendererTypeNameSimple(){return e.rendererTypeNameState??(0,c.getConf)(e,"defaultRendering")},get filters(){},get scaleType(){return e.scale??(0,c.getConf)(e,"scaleType")},get maxScore(){return e.constraints.max??(0,c.getConf)(e,"maxScore")},get minScore(){return e.constraints.min??(0,c.getConf)(e,"minScore")}}))).views((e=>({get 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g.types.compose("MultiLinearWiggleDisplay",O(t),g.types.model({type:g.types.literal("MultiLinearWiggleDisplay"),layout:g.types.optional(g.types.frozen(),[])})).volatile((()=>({featureUnderMouseVolatile:void 0,sourcesVolatile:void 0}))).actions((e=>({setLayout(t){e.layout=t},clearLayout(){e.layout=[]},setSources(t){J()(t,e.sourcesVolatile)||(e.sourcesVolatile=t)},setFeatureUnderMouse(t){e.featureUnderMouseVolatile=t}}))).views((e=>({get featureUnderMouse(){return e.featureUnderMouseVolatile},get TooltipComponent(){return Y},get rendererTypeName(){const t=e.rendererTypeNameSimple,r=Q.get(t);if(!r)throw new Error(`unknown renderer ${t}`);return r}}))).views((e=>({get needsScalebar(){return"MultiXYPlotRenderer"===e.rendererTypeName||"MultiRowXYPlotRenderer"===e.rendererTypeName||"MultiLineRenderer"===e.rendererTypeName||"MultiRowLineRenderer"===e.rendererTypeName},get needsFullHeightScalebar(){return"MultiXYPlotRenderer"===e.rendererTypeName||"MultiLineRenderer"===e.rendererTypeName},get 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e.save(),n.forEach((r=>{const{reducedFeatures:n}=M(e,{...t,features:l[r.name]||[],height:c,colorCallback:()=>r.color||"blue"});e.strokeStyle="rgba(200,200,200,0.8)",e.beginPath(),e.moveTo(0,c),e.lineTo(d,c),e.stroke(),e.translate(0,c),u=u.concat(n)})),e.restore(),{reducedFeatures:u}}}const ae=(0,c.ConfigurationSchema)("MultiRowXYPlotRenderer",{filled:{type:"boolean",defaultValue:!0},displayCrossHatches:{type:"boolean",description:"choose to draw cross hatches (sideways lines)",defaultValue:!1},summaryScoreMode:{type:"stringEnum",model:g.types.enumeration("Score type",["max","min","avg","whiskers"]),description:"choose whether to use max/min/average or whiskers which combines all three into the same rendering",defaultValue:"whiskers"},minSize:{type:"number",defaultValue:0}},{baseConfiguration:h,explicitlyTyped:!0}),oe=(0,c.ConfigurationSchema)("MultiDensityRenderer",{},{baseConfiguration:h,explicitlyTyped:!0});class ie extends s{async draw(e,t){const{sources:r,features:n}=t,a=(0,i.groupBy)(n.values(),(e=>e.get("source"))),o=t.height/r.length;let s=[];return e.save(),r.forEach((r=>{const n=a[r.name]||[],{reducedFeatures:i}=b(e,{...t,features:n,height:o});e.translate(0,o),s=s.concat(i)})),e.restore(),{reducedFeatures:s}}}class se extends s{async draw(e,t){const{sources:r,features:n}=t,a=(0,i.groupBy)(n.values(),(e=>e.get("source")));let o=[];return r.forEach((r=>{const{reducedFeatures:n}=N(e,{...t,features:a[r.name]||[],colorCallback:()=>r.color||"blue"});o=o.concat(n)})),{reducedFeatures:o}}}const le=(0,c.ConfigurationSchema)("MultiLineRenderer",{displayCrossHatches:{type:"boolean",description:"choose to draw cross hatches (sideways lines)",defaultValue:!1},summaryScoreMode:{type:"stringEnum",model:g.types.enumeration("Score type",["max","min","avg","whiskers"]),description:"choose whether to use max/min/average or whiskers which combines all three into the same rendering",defaultValue:"avg"}},{baseConfiguration:h,explicitlyTyped:!0});class ce extends s{async draw(e,t){const{bpPerPx:r,sources:n,regions:a,features:o}=t,s=a[0],l=(0,i.groupBy)(o.values(),(e=>e.get("source"))),c=t.height/n.length,d=(s.end-s.start)/r;let u=[];return e.save(),n.forEach((r=>{const{reducedFeatures:n}=N(e,{...t,features:l[r.name]||[],height:c,colorCallback:()=>r.color||"blue"});e.strokeStyle="rgba(200,200,200,0.8)",e.beginPath(),e.moveTo(0,c),e.lineTo(d,c),e.stroke(),e.translate(0,c),u=u.concat(n)})),e.restore(),{reducedFeatures:u}}}const de=(0,c.ConfigurationSchema)("MultiRowLineRenderer",{displayCrossHatches:{type:"boolean",description:"choose to draw cross hatches (sideways lines)",defaultValue:!1},summaryScoreMode:{type:"stringEnum",model:g.types.enumeration("Score type",["max","min","avg","whiskers"]),description:"choose whether to use max/min/average or whiskers which combines all three into the same rendering",defaultValue:"avg"}},{baseConfiguration:h,explicitlyTyped:!0}),ue=(0,C.lazy)((()=>r.e(9305).then(r.bind(r,69305))));var pe=r(58921),me=r(2406),ge=r(93100),he=r(3496);class fe extends me.A{name="MultiWiggleGetSources";async deserializeArguments(e,t){return{...await super.deserializeArguments(e,t),filters:e.filters?new ge.A({filters:e.filters}):void 0}}async serializeArguments(e,t){const r=this.pluginManager,n=r.rootModel?.session?.assemblyManager;if(!n)return e;const a=await(0,i.renameRegionsIfNeeded)(n,{...e,filters:e.filters?.toJSON().filters});return super.serializeArguments(a,t)}async execute(e,t){const r=this.pluginManager,n=await this.deserializeArguments(e,t),{regions:a,adapterConfig:o,sessionId:i}=n,{dataAdapter:s}=await(0,he.cK)(r,i,o);return s.getSources(a,n)}}class ye extends me.A{name="WiggleGetMultiRegionQuantitativeStats";async deserializeArguments(e,t){return{...await super.deserializeArguments(e,t),filters:e.filters?new ge.A({filters:e.filters}):void 0}}async serializeArguments(e,t){const r=this.pluginManager,n=r.rootModel?.session?.assemblyManager;if(!n)return e;const a=await(0,i.renameRegionsIfNeeded)(n,{...e,filters:e.filters?.toJSON().filters});return super.serializeArguments(a,t)}async execute(e,t){const r=this.pluginManager,n=await this.deserializeArguments(e,t),{regions:a,adapterConfig:o,sessionId:i}=n,{dataAdapter:s}=await(0,he.cK)(r,i,o);return s.getMultiRegionQuantitativeStats(a,n)}}class be extends me.A{name="WiggleGetGlobalQuantitativeStats";async deserializeArguments(e,t){return{...await super.deserializeArguments(e,t),filters:e.filters?new ge.A({filters:e.filters}):void 0}}async execute(e,t){const r=this.pluginManager,n=await this.deserializeArguments(e,t),{adapterConfig:a,sessionId:o}=n,{dataAdapter:i}=await(0,he.cK)(r,o,a);return i.getGlobalStats(n)}}class we extends n.A{name="WigglePlugin";install(e){e.addAdapterType((()=>new l.A({name:"MultiWiggleAdapter",displayName:"Multi-wiggle adapter",configSchema:m,adapterCapabilities:["hasResolution","hasLocalStats","hasGlobalStats"],adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>r.e(1822).then(r.bind(r,31822)).then((e=>e.default))}))),e.addAdapterType((()=>new l.A({name:"BigWigAdapter",displayName:"BigWig adapter",configSchema:d,adapterCapabilities:["hasResolution","hasLocalStats","hasGlobalStats"],getAdapterClass:()=>Promise.all([r.e(3902),r.e(4234)]).then(r.bind(r,14234)).then((e=>e.default))}))),function(e){e.addTrackType((()=>{const t=function(e){return(0,c.ConfigurationSchema)("QuantitativeTrack",{},{baseConfiguration:(0,u.createBaseTrackConfig)(e)})}(e);return new p.A({name:"QuantitativeTrack",displayName:"Quantitative track",configSchema:t,stateModel:(0,u.createBaseTrackModel)(e,"QuantitativeTrack",t)})}))}(e),function(e){e.addTrackType((()=>{const t=(e=>(0,c.ConfigurationSchema)("MultiQuantitativeTrack",{},{baseConfiguration:(0,u.createBaseTrackConfig)(e)}))(e);return new p.A({name:"MultiQuantitativeTrack",displayName:"Multi-quantitative track",configSchema:t,stateModel:(0,u.createBaseTrackModel)(e,"MultiQuantitativeTrack",t)})}))}(e),function(e){e.addDisplayType((()=>{const t=function(e){const t=e.getRendererType("XYPlotRenderer").configSchema,r=e.getRendererType("DensityRenderer").configSchema,n=e.getRendererType("LinePlotRenderer").configSchema;return(0,c.ConfigurationSchema)("LinearWiggleDisplay",{defaultRendering:{type:"stringEnum",model:g.types.enumeration("Rendering",["density","xyplot","line"]),defaultValue:"xyplot"},renderers:(0,c.ConfigurationSchema)("RenderersConfiguration",{DensityRenderer:r,XYPlotRenderer:t,LinePlotRenderer:n})},{baseConfiguration:B(),explicitlyTyped:!0})}(e),n=G(e,t);return new L.A({name:"LinearWiggleDisplay",displayName:"Wiggle display",configSchema:t,stateModel:n,trackType:"QuantitativeTrack",viewType:"LinearGenomeView",ReactComponent:(0,C.lazy)((()=>Promise.resolve().then(r.bind(r,98911))))})}))}(e),function(e){e.addDisplayType((()=>{const t=function(e){const t=e.getRendererType("MultiXYPlotRenderer").configSchema,r=e.getRendererType("MultiDensityRenderer").configSchema,n=e.getRendererType("MultiRowXYPlotRenderer").configSchema,a=e.getRendererType("MultiLineRenderer").configSchema,o=e.getRendererType("MultiRowLineRenderer").configSchema;return(0,c.ConfigurationSchema)("MultiLinearWiggleDisplay",{defaultRendering:{type:"stringEnum",model:g.types.enumeration("Rendering",["multirowxy","xyplot","multirowdensity","multiline","multirowline"]),defaultValue:"multirowxy"},renderers:(0,c.ConfigurationSchema)("RenderersConfiguration",{MultiXYPlotRenderer:t,MultiDensityRenderer:r,MultiRowXYPlotRenderer:n,MultiLineRenderer:a,MultiRowLineRenderer:o}),height:{type:"number",defaultValue:200}},{baseConfiguration:B(),explicitlyTyped:!0})}(e);return new L.A({name:"MultiLinearWiggleDisplay",displayName:"Multi-wiggle display",configSchema:t,stateModel:Z(0,t),trackType:"MultiQuantitativeTrack",viewType:"LinearGenomeView",ReactComponent:(0,C.lazy)((()=>r.e(8526).then(r.bind(r,8526))))})}))}(e),function(e){e.addRendererType((()=>new F({name:"LinePlotRenderer",ReactComponent:k,configSchema:I,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new E({name:"XYPlotRenderer",ReactComponent:k,configSchema:R,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new w({name:"DensityRenderer",ReactComponent:k,configSchema:f,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new te({name:"MultiXYPlotRenderer",ReactComponent:ee,configSchema:re,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new ne({name:"MultiRowXYPlotRenderer",ReactComponent:ee,configSchema:ae,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new ie({name:"MultiDensityRenderer",ReactComponent:ee,configSchema:oe,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new se({name:"MultiLineRenderer",ReactComponent:ee,configSchema:le,pluginManager:e})))}(e),function(e){e.addRendererType((()=>new ce({name:"MultiRowLineRenderer",ReactComponent:ee,configSchema:de,pluginManager:e})))}(e),function(e){e.addAddTrackWorkflowType((()=>new pe.AddTrackWorkflowType({name:"Multi-wiggle track",ReactComponent:(0,C.lazy)((()=>r.e(2018).then(r.bind(r,52018)))),stateModel:g.types.model({})})))}(e),function(e){e.addToExtensionPoint("TrackSelector-multiTrackMenuItems",((e,t)=>{const{session:r}=t;return[...e,...(0,i.isSessionWithAddTracks)(r)?[{label:"Create multi-wiggle track",onClick:e=>{const t=e.selection,r=t.map((e=>(0,c.readConfObject)(e,"name")));(0,i.getSession)(e).queueDialog((n=>[ue,{tracks:t,onClose:(a,o)=>{a&&o&&function(n){const a=t.map((e=>(0,c.readConfObject)(e,"adapter"))).map(((e,t)=>({...e,source:r[t]}))),o=[...new Set(t.flatMap((e=>(0,c.readConfObject)(e,"assemblyNames"))))],s=`multitrack-${+Date.now()}-sessionTrack`,l=(0,i.getSession)(e);(0,i.isSessionWithAddTracks)(l)&&(l.addTrackConf({type:"MultiQuantitativeTrack",trackId:s,name:n.name,assemblyNames:o,adapter:{type:"MultiWiggleAdapter",subadapters:a}}),e.view.showTrack(s))}(o),n()}}]))}}]:[]]}))}(e),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const o="BigWigAdapter",i=(0,a.getFileName)(t),s={type:o,bigWigLocation:t};return/\.(bw|bigwig)$/i.test(i)&&!n||n===o?s:e(t,r,n)})),e.addToExtensionPoint("Core-guessTrackTypeForLocation",(e=>t=>"BigWigAdapter"===t?"QuantitativeTrack":e(t))),e.addRpcMethod((()=>new be(e))),e.addRpcMethod((()=>new ye(e))),e.addRpcMethod((()=>new fe(e)))}exports={LinearWiggleDisplayReactComponent:q.default,XYPlotRendererReactComponent:k,XYPlotRenderer:E,WiggleBaseRenderer:s,linearWiggleDisplayModelFactory:G,xyPlotRendererConfigSchema:R,utils:y}}},90461:(e,t,r)=>{"use strict";r.d(t,{A:()=>l});var n=r(7552),a=r(48231),o=r(68446),i=r(77126);function s(){return s=Object.assign?Object.assign.bind():function(e){for(var t=1;t<arguments.length;t++){var r=arguments[t];for(var n in r)({}).hasOwnProperty.call(r,n)&&(e[n]=r[n])}return e},s.apply(null,arguments)}const l=(0,o.observer)((function({model:e,orientation:t}){const{ticks:r}=e,o=(0,a.A)();return r?n.createElement(i.Axis,s({},r,{shadow:2,format:e=>e,style:{orient:"left"===t?i.LEFT:i.RIGHT},bg:o.palette.background.default,fg:o.palette.text.primary})):null}))},75429:(e,t,r)=>{"use strict";r.r(t),r.d(t,{YSCALEBAR_LABEL_OFFSET:()=>u,fillRectCtx:()=>w,getNiceDomain:()=>g,getOrigin:()=>m,getQuantitativeStats:()=>h,getScale:()=>p,quantitativeStatsAutorun:()=>f,round:()=>b,toP:()=>y});var n=r(45824),a=r(35873),o=r(6754),i=r(42489),s=r(99546),l=r(91468),c=r(36422),d=r(68584);const u=5;function p({domain:e=[],range:t=[],scaleType:r,pivotValue:i,inverted:s}){let l;const[c,d]=e;if(void 0===c||void 0===d)throw new Error("invalid 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f(e){(0,c.addDisposer)(e,(0,i.autorun)((async()=>{try{const t=new AbortController,r=(0,s.getContainingView)(e);if(e.setLoading(t),!r.initialized||!e.featureDensityStatsReady||e.regionTooLarge||e.error)return;const n=JSON.stringify(r.dynamicBlocks),a=await h(e,{signal:t.signal,filters:[],...e.renderProps()});(0,c.isAlive)(e)&&e.updateQuantitativeStats(a,n)}catch(t){!(0,s.isAbortException)(t)&&(0,c.isAlive)(e)&&(console.error(t),e.setError(t))}}),{delay:1e3}))}function y(e=0){return+(+e).toPrecision(6)}function b(e){return Math.round(1e5*e)/1e5}function w(e,t,r,n,a,o){r<0&&(e+=r,r=-r),n<0&&(t+=n,n=-n),o&&(a.fillStyle=o),a.fillRect(e,t,r,n)}},63163:(e,t,r)=>{"use strict";r.d(t,{A:()=>Mo});var n=r(82727),a=r(12678),o=r(92070),i=r(68584),s=r(1622);const l=(0,i.ConfigurationSchema)("OAuthInternetAccount",{tokenType:{description:"a custom name for a token to include in the header",type:"string",defaultValue:"Bearer"},authEndpoint:{description:"the authorization code endpoint of the internet 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g(e,t){return e.refresh_token&&t(e.refresh_token),e.access_token}async function h({response:e,reason:t,statusText:r}){return[`HTTP ${e.status}`,t,r??await f(e)].filter((e=>!!e)).join(" - ")}async function f(e){try{return await e.text()}catch(t){return e.statusText}}const y=e=>s.InternetAccount.named("OAuthInternetAccount").props({type:d.types.literal("OAuthInternetAccount"),configuration:(0,i.ConfigurationReference)(e)}).views((()=>{let e;return{get codeVerifierPKCE(){if(e)return e;const t=new Uint8Array(32);return globalThis.crypto.getRandomValues(t),e=p(u.hp.from(t).toString("base64")),e}}})).views((e=>({get authEndpoint(){return(0,i.getConf)(e,"authEndpoint")},get tokenEndpoint(){return(0,i.getConf)(e,"tokenEndpoint")},get needsPKCE(){return(0,i.getConf)(e,"needsPKCE")},get clientId(){return(0,i.getConf)(e,"clientId")},get scopes(){return(0,i.getConf)(e,"scopes")},state:()=>(0,i.getConf)(e,"state"),get responseType(){return(0,i.getConf)(e,"responseType")},get 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URL(e.authEndpoint);s.search=i.toString();const l=`JBrowseAuthWindow-${e.internetAccountId}`;if(c.isElectron){const{ipcRenderer:r}=window.require("electron"),a=await r.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:o,url:s.toString()}),i=new MessageEvent("message",{data:{name:l,redirectUri:a}});this.finishOAuthWindow(i,t,n)}else window.open(s,l,"width=500,height=600,left=0,top=0")},async getTokenFromUser(t,r){const n=e.retrieveRefreshToken();let a=!0;if(n)try{t(await e.exchangeRefreshForAccessToken(n)),a=!1}catch(t){console.error(t),e.removeRefreshToken()}a&&(this.addMessageChannel(t,r),this.useEndpointForAuthorization(t,r))},async validateToken(t,r){const a=e.addAuthHeaderToInit({method:"HEAD"},t),o=await fetch(r.uri,a);if(!o.ok){e.removeToken();const t=e.retrieveRefreshToken();if(t)try{n||(n=e.exchangeRefreshForAccessToken(t));const r=await n;return n=void 0,r}catch(e){console.error("Token could not be refreshed",e)}throw new Error(await h({response:o,reason:"Error validating token"}))}return t}}})).actions((e=>{const t=e.getFetcher;return{getFetcher(r){const n=t(r);return async(t,a)=>(r&&await e.validateToken(await e.getToken(r),r),n(t,a))}}})),b=(0,i.ConfigurationSchema)("ExternalTokenInternetAccount",{validateWithHEAD:{description:"validate the token with a HEAD request before using it",type:"boolean",defaultValue:!0}},{baseConfiguration:s.BaseInternetAccountConfig,explicitlyTyped:!0});var w=r(7552),v=r(29499),C=r(1343),S=r(58507),k=r(5401),T=r(49823);const x=({internetAccountId:e,handleClose:t})=>{const[r,n]=(0,w.useState)("");return w.createElement(T.Dialog,{open:!0,maxWidth:"xl","data-testid":"externalToken-form",title:`Enter token for ${e}`},w.createElement(v.A,{style:{display:"flex",flexDirection:"column"}},w.createElement(C.A,{required:!0,label:"Enter 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Error(`Token could not be validated — ${a.status} ${e?` (${e})`:""}`)}return t}}))),P=(0,i.ConfigurationSchema)("HTTPBasicInternetAccount",{tokenType:{description:"a custom name for a token to include in the header",type:"string",defaultValue:"Basic"},validateWithHEAD:{description:"validate the token with a HEAD request before using it",type:"boolean",defaultValue:!0}},{baseConfiguration:s.BaseInternetAccountConfig,explicitlyTyped:!0});function M({internetAccountId:e,handleClose:t}){const[r,n]=(0,w.useState)(""),[a,o]=(0,w.useState)("");return w.createElement(T.Dialog,{open:!0,maxWidth:"xl","data-testid":"login-httpbasic",title:`Log in for ${e}`},w.createElement("form",{onSubmit:e=>{r&&a?t(btoa(`${r}:${a}`)):t(),e.preventDefault()}},w.createElement(v.A,{style:{display:"flex",flexDirection:"column"}},w.createElement(C.A,{required:!0,label:"Username",variant:"outlined",inputProps:{"data-testid":"login-httpbasic-username"},onChange:e=>{n(e.target.value)},margin:"dense"}),w.createElement(C.A,{required:!0,label:"Password",type:"password",autoComplete:"current-password",variant:"outlined",inputProps:{"data-testid":"login-httpbasic-password"},onChange:e=>{o(e.target.value)},margin:"dense"})),w.createElement(S.A,null,w.createElement(k.A,{variant:"contained",color:"primary",type:"submit"},"Submit"),w.createElement(k.A,{variant:"contained",color:"secondary",type:"submit",onClick:()=>{t()}},"Cancel"))))}const E=e=>s.InternetAccount.named("HTTPBasicInternetAccount").props({type:d.types.literal("HTTPBasicInternetAccount"),configuration:(0,i.ConfigurationReference)(e)}).views((e=>({get validateWithHEAD(){return(0,i.getConf)(e,"validateWithHEAD")}}))).actions((e=>({getTokenFromUser(t,r){const{session:n}=(0,d.getRoot)(e);n.queueDialog((n=>[M,{internetAccountId:e.internetAccountId,handleClose:e=>{e?t(e):r(new Error("User cancelled entry")),n()}}]))},async validateToken(t,r){if(!e.validateWithHEAD)return t;const n=e.addAuthHeaderToInit({method:"HEAD"},t),a=await fetch(r.uri,n);if(!a.ok)throw new Error(await h({response:a,reason:"Error validating token"}));return t}}))),R=(0,i.ConfigurationSchema)("DropboxOAuthInternetAccount",{authEndpoint:{description:"the authorization code endpoint of the internet account",type:"string",defaultValue:"https://www.dropbox.com/oauth2/authorize"},tokenEndpoint:{description:"the token endpoint of the internet account",type:"string",defaultValue:"https://api.dropbox.com/oauth2/token"},needsPKCE:{description:"boolean to indicate if the endpoint needs a PKCE code",type:"boolean",defaultValue:!0},domains:{description:"array of valid domains the url can contain to use this account",type:"stringArray",defaultValue:["addtodropbox.com","db.tt","dropbox.com","dropboxapi.com","dropboxbusiness.com","dropbox.tech","getdropbox.com"]}},{baseConfiguration:l,explicitlyTyped:!0}),I={shared_link_not_found:"The shared link wasn't found.",shared_link_access_denied:"The caller is not allowed to access this shared link.",unsupported_link_type:"This type of link is not supported; use files/export instead.",shared_link_is_directory:"Directories cannot be retrieved by this endpoint."};async function N(e,t){let r="";try{const t=JSON.parse(await e.text()).error[".tag"];r=I[t]||t}catch(e){}return h({response:e,reason:t,statusText:r})}var F=r(2859);function L(e){return w.createElement(F.A,e,w.createElement("path",{d:"M3 6.2L8 9.39L13 6.2L8 3L3 6.2M13 6.2L18 9.39L23 6.2L18 3L13 6.2M3 12.55L8 15.74L13 12.55L8 9.35L3 12.55M18 9.35L13 12.55L18 15.74L23 12.55L18 9.35M8.03 16.8L13.04 20L18.04 16.8L13.04 13.61L8.03 16.8Z"}))}const D=e=>y(l).named("DropboxOAuthInternetAccount").props({type:d.types.literal("DropboxOAuthInternetAccount"),configuration:(0,i.ConfigurationReference)(e)}).views((()=>({get toggleContents(){return w.createElement(L,null)},get selectorLabel(){return"Enter Dropbox share link"}}))).actions((e=>({getFetcher:t=>async(r,n)=>{const a=await e.getToken(t),o=e.addAuthHeaderToInit({...n,method:"POST"},a);o.headers.append("Dropbox-API-Arg",JSON.stringify({url:r}));const i=await fetch("https://content.dropboxapi.com/2/sharing/get_shared_link_file",o);if(!i.ok)throw new Error(await N(i));return i},async validateToken(t,r){const n=await fetch("https://api.dropboxapi.com/2/sharing/get_shared_link_metadata",{method:"POST",headers:{Authorization:`Bearer ${t}`,"Content-Type":"application/json"},body:JSON.stringify({url:r.uri})});if(!n.ok){const t=e.retrieveRefreshToken();if(t){e.removeRefreshToken();const n=await e.exchangeRefreshForAccessToken(t);return this.validateToken(n,r)}throw new Error(await N(n,"Token could not be validated"))}return t}}))),B=(0,i.ConfigurationSchema)("GoogleDriveOAuthInternetAccount",{authEndpoint:{description:"the authorization code endpoint of the internet account",type:"string",defaultValue:"https://accounts.google.com/o/oauth2/v2/auth"},scopes:{description:"optional scopes for the authorization call",type:"string",defaultValue:"https://www.googleapis.com/auth/drive.readonly"},domains:{description:"array of valid domains the url can contain to use this account",type:"stringArray",defaultValue:['drive.google.com"']},responseType:{description:"the type of response from the authorization endpoint",type:"string",defaultValue:"token"}},{baseConfiguration:l,explicitlyTyped:!0});async function V(e,t){let r="";try{r=JSON.parse(await e.text()).error.message}catch(e){}return h({response:e,reason:t,statusText:r})}var z=r(99834);class O extends z.RemoteFileWithRangeCache{constructor(e,t){super(e,t),this.statsPromise=this.fetch(e,{metadataOnly:!0}).then((e=>e.json()))}async fetch(e,t){return super.fetch(e,t)}async stat(){return this.statsPromise}}function H(e){return w.createElement(F.A,e,w.createElement("path",{d:"M7.71,3.5L1.15,15L4.58,21L11.13,9.5M9.73,15L6.3,21H19.42L22.85,15M22.28,14L15.42,2H8.58L8.57,2L15.43,14H22.28Z"}))}function j(e){return`https://www.googleapis.com/drive/v3/files/${/[-\w]{25,}/.exec(e)}`}function W(e){return y(l).named("GoogleDriveOAuthInternetAccount").props({type:d.types.literal("GoogleDriveOAuthInternetAccount"),configuration:(0,i.ConfigurationReference)(e)}).views((()=>({get toggleContents(){return w.createElement(H,null)},get selectorLabel(){return"Enter Google Drive share link"}}))).actions((e=>({getFetcher:t=>async(r,n)=>{const a=new URL(j(String(r))),o=new URLSearchParams;n?.metadataOnly?o.append("fields","size"):o.append("alt","media"),a.search=o.toString();const i=await e.getToken(t),s=await fetch(a,e.addAuthHeaderToInit({...n,method:"GET",credentials:"same-origin"},i));if(!s.ok)throw new Error(await V(s));return s},openLocation(e){return new O(e.uri,{fetch:this.getFetcher(e)})},async validateToken(e,t){const r=await fetch(j(t.uri),{headers:{Authorization:`Bearer ${e}`,"Content-Type":"application/x-www-form-urlencoded"}});if(!r.ok)throw new Error(await V(r,"Token could not be validated"));return e}})))}class G extends a.A{name="AuthenticationPlugin";exports={OAuthConfigSchema:l,OAuthInternetAccountModelFactory:y,ExternalTokenConfigSchema:b,ExternalTokenInternetAccountModelFactory:A,HTTPBasicConfigSchema:P,HTTPBasicInternetAccountModelFactory:E,DropboxOAuthConfigSchema:R,DropboxOAuthInternetAccountModelFactory:D,GoogleDriveOAuthConfigSchema:B,GoogleDriveOAuthInternetAccountModelFactory:W};install(e){e.addInternetAccountType((()=>new o.A({name:"OAuthInternetAccount",configSchema:l,stateModel:y(l)}))),e.addInternetAccountType((()=>new o.A({name:"ExternalTokenInternetAccount",configSchema:b,stateModel:A(b)}))),e.addInternetAccountType((()=>new o.A({name:"HTTPBasicInternetAccount",configSchema:P,stateModel:E(P)}))),e.addInternetAccountType((()=>new o.A({name:"DropboxOAuthInternetAccount",configSchema:R,stateModel:D(R)}))),e.addInternetAccountType((()=>new o.A({name:"GoogleDriveOAuthInternetAccount",configSchema:B,stateModel:W(B)})))}}var $=r(47369);const q=(0,i.ConfigurationSchema)("BigBedAdapter",{bigBedLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bb",locationType:"UriLocation"}},scoreColumn:{type:"string",description:'The column to use as a "score" attribute',defaultValue:""},aggregateField:{type:"string",description:"An attribute to aggregate features with",defaultValue:"geneName"}},{explicitlyTyped:!0}),_=(0,i.ConfigurationSchema)("BedpeAdapter",{bedpeLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bedpe.gz",locationType:"UriLocation"}},columnNames:{type:"stringArray",description:"List of column names",defaultValue:[]}},{explicitlyTyped:!0}),U=(0,i.ConfigurationSchema)("BedTabixAdapter",{bedGzLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz",locationType:"UriLocation"}},index:(0,i.ConfigurationSchema)("TabixIndex",{indexType:{model:d.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi",locationType:"UriLocation"}}}),columnNames:{type:"stringArray",description:"List of column names",defaultValue:[]},scoreColumn:{type:"string",description:'The column to use as a "score" attribute',defaultValue:""},autoSql:{type:"string",description:"The autoSql definition for the data fields in the file",defaultValue:""}},{explicitlyTyped:!0}),J=(0,i.ConfigurationSchema)("BedAdapter",{bedLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz",locationType:"UriLocation"}},columnNames:{type:"stringArray",description:"List of column names",defaultValue:[]},scoreColumn:{type:"string",description:'The column to use as a "score" attribute',defaultValue:""},autoSql:{type:"string",description:"The autoSql definition for the data fields in the file",defaultValue:""},colRef:{type:"number",description:'The column to use as a "refName" attribute',defaultValue:0},colStart:{type:"number",description:'The column to use as a "start" attribute',defaultValue:1},colEnd:{type:"number",description:'The column to use as a "end" attribute',defaultValue:2}},{explicitlyTyped:!0});var X=r(91468);class Y extends a.A{name="BedPlugin";install(e){!function(e){e.addAdapterType((()=>new $.A({name:"BigBedAdapter",displayName:"BigBed adapter",configSchema:q,getAdapterClass:()=>Promise.all([r.e(972),r.e(3902),r.e(6834)]).then(r.bind(r,6834)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"BedAdapter",displayName:"BED adapter",configSchema:J,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(4499),r.e(972),r.e(4864)]).then(r.bind(r,34864)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"BedpeAdapter",displayName:"BEDPE adapter",configSchema:_,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(4499),r.e(14)]).then(r.bind(r,10014)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"BedTabixAdapter",displayName:"BED tabix adapter",configSchema:U,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(8120),r.e(972),r.e(6214)]).then(r.bind(r,86214)).then((e=>e.default))})))}(e),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="BigBedAdapter",o=(0,X.getFileName)(t),i={type:a,bigBedLocation:t};return/\.(bb|bigbed)$/i.test(o)&&!n||n===a?i:e(t,r,n)})),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="BedpeAdapter",o=(0,X.getFileName)(t);return/\.bedpe(\.gz)?$/i.test(o)||n===a?{type:a,bedpeLocation:t}:e(t,r,n)})),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="BedTabixAdapter",o=(0,X.getFileName)(t),i=r&&(0,X.getFileName)(r);return/\.bed\.b?gz$/i.test(o)||n===a?{type:a,bedGzLocation:t,index:{location:r||(0,X.makeIndex)(t,".tbi"),indexType:(0,X.makeIndexType)(i,"CSI","TBI")}}:e(t,r,n)})),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="BedAdapter",o=(0,X.getFileName)(t);return/\.bed$/i.test(o)||n===a?{type:a,bedLocation:t}:e(t,r,n)})),e.addToExtensionPoint("Core-guessTrackTypeForLocation",(e=>t=>"BedpeAdapter"===t?"VariantTrack":e(t)))}}var K=r(8832),Q=r(58921);const Z=(0,i.ConfigurationSchema)("BreakpointAlignmentsWidget",{}),ee=d.types.model("BreakpointAlignmentsWidget",{id:K.ElementId,type:d.types.literal("BreakpointAlignmentsWidget"),featureData:d.types.frozen()}).actions((e=>({setFeatureData(t){e.featureData=t},clearFeatureData(){e.featureData=void 0}})));var te=r(63589),re=r(9502);class ne extends te.A{getBreakendCoveringRegions({feature:e,assembly:t}){const r=e.get("ALT")?.[0],n=r?(0,re.h)(r):void 0,a=e.get("start"),o=e.get("refName");let i,s;if("<TRA>"===r){const t=e.get("INFO");i=t.END[0]-1,s=t.CHR2[0]}else if(n?.MatePosition){const e=n.MatePosition.split(":");i=+e[1]-1,s=e[0]}else if(e.get("mate")){const t=e.get("mate");s=t.refName,i=t.start}else i=a+1;if(!s)throw new Error(`unable to resolve mate refName ${s} in reference genome`);return{pos:a,refName:t.getCanonicalRefName(o),mateRefName:t.getCanonicalRefName(s),matePos:i}}singleLevelSnapshotFromBreakendFeature(e,t){const r=(0,c.getSession)(t),{assemblyName:n}=t.displayedRegions[0],{assemblyManager:a}=r,o=a.get(n);if(!o)throw new Error(`assembly ${n} not found`);if(!o.regions)throw new Error(`assembly ${n} regions not loaded`);const{refName:i,pos:s,mateRefName:l,matePos:d}=this.getBreakendCoveringRegions({feature:e,assembly:o}),u=o.regions.find((e=>e.refName===i)),p=o.regions.find((e=>e.refName===l)),m=[{...u},{...u}],g=[{...p},{...p}];return m[0].end=s,m[1].start=s,g[0].end=d,g[1].start=d,{type:"BreakpointSplitView",views:[{type:"LinearGenomeView",displayedRegions:m,hideHeader:!0,bpPerPx:10,offsetPx:(u.start+e.get("start"))/10}],displayName:`${e.get("name")||e.get("id")||"breakend"} split detail`,featureData:void 0}}snapshotFromBreakendFeature(e,t){const r=(0,c.getSession)(t),{assemblyName:n}=t.displayedRegions[0],{assemblyManager:a}=r,o=a.get(n);if(!o)throw new Error(`assembly ${n} not found`);if(!o.regions)throw new Error(`assembly ${n} regions not loaded`);const{refName:i,pos:s,mateRefName:l,matePos:d}=this.getBreakendCoveringRegions({feature:e,assembly:o}),u=o.regions.find((e=>e.refName===i)),p=o.regions.find((e=>e.refName===l)),m=[{...u},{...u}],g=[{...p},{...p}];return m[0].end=s,m[1].start=s,g[0].end=d,g[1].start=d,{type:"BreakpointSplitView",views:[{type:"LinearGenomeView",displayedRegions:m,hideHeader:!0,bpPerPx:10,offsetPx:(u.start+e.get("start"))/10},{type:"LinearGenomeView",displayedRegions:g,hideHeader:!0,bpPerPx:10,offsetPx:(p.start+d)/10}],displayName:`${e.get("name")||e.get("id")||"breakend"} split detail`}}}var ae=r(42489),oe=r(45465),ie=r(64502),se=r(75441),le=r(49473);const ce=(0,w.lazy)((()=>r.e(7790).then(r.bind(r,47790))));function de(e,t){return e.displays[0].searchFeatureByID?.(t.id())}async function ue(e,t){const{views:r}=e,{rpcManager:n,assemblyManager:a}=(0,c.getSession)(e),o=e.views[0]?.assemblyNames[0];if(!o)return;if(!await a.waitForAssembly(o))return;const s=t.configuration.trackId;return Promise.all(r.map((async e=>(await n.call(s,"CoreGetFeatures",{adapterConfig:(0,i.getConf)(t,["adapter"]),sessionId:s,regions:e.staticBlocks.contentBlocks})).flat())))}function pe(e){return d.types.compose("BreakpointSplitView",s.BaseViewModel,d.types.model({type:d.types.literal("BreakpointSplitView"),height:d.types.optional(d.types.refinement("viewHeight",d.types.number,(e=>e>=40)),400),trackSelectorType:"hierarchical",showIntraviewLinks:!0,linkViews:!1,interactToggled:!1,views:d.types.array(e.getViewType("LinearGenomeView").stateModel)})).volatile((()=>({width:800,matchedTrackFeatures:{}}))).views((e=>({async exportSvg(t={}){const{renderToSvg:n}=await Promise.all([r.e(5727),r.e(5668)]).then(r.bind(r,95668)),a=await n(e,t),o=new Blob([a],{type:"image/svg+xml"});(0,oe.saveAs)(o,t.filename||"image.svg")}}))).views((e=>({get matchedTracks(){return 1===e.views.length?e.views[0].tracks:(0,le.y$)((e=>e.configuration.trackId),...e.views.map((e=>e.tracks)))},getMatchedTracks:t=>e.views.map((e=>e.getTrack(t))).filter((e=>!!e)),hasTranslocations(e){return[...this.getTrackFeatures(e).values()].find((e=>"translocation"===e.get("type")))},hasPairedFeatures(e){return[...this.getTrackFeatures(e).values()].find((e=>"paired_feature"===e.get("type")))},getTrackFeatures:t=>new Map(e.matchedTrackFeatures[t]?.flat().map((e=>[e.id(),e]))),getMatchedFeaturesInLayout(e,t){const r=this.getMatchedTracks(e);return t.map((e=>e.map((e=>{const t=r.findIndex((t=>de(t,e)));return-1!==t?{feature:e,layout:de(r[t],e),level:t}:void 0})).filter(c.notEmpty)))}}))).actions((e=>({afterAttach(){(0,d.addDisposer)(e,(0,d.onAction)(e,(({name:t,path:r,args:n})=>{e.linkViews&&["horizontalScroll","zoomTo","setScaleFactor","showTrack","toggleTrack","hideTrack","setTrackLabels","toggleCenterLine"].includes(t)&&r&&this.onSubviewAction(t,r,n)})))},onSubviewAction(t,r,n){e.views.forEach((e=>{(0,d.getPath)(e).endsWith(r)||e[t](n?.[0])}))},setWidth(t){e.width=t,e.views.forEach((e=>{e.setWidth(t)}))},removeView(t){e.views.remove(t)},toggleInteract(){e.interactToggled=!e.interactToggled},toggleIntraviewLinks(){e.showIntraviewLinks=!e.showIntraviewLinks},toggleLinkViews(){e.linkViews=!e.linkViews},setMatchedTrackFeatures(t){e.matchedTrackFeatures=t},reverseViewOrder(){e.views.reverse()}}))).actions((e=>({afterAttach(){(0,d.addDisposer)(e,(0,ae.autorun)((async()=>{try{if(!e.views.every((e=>e.initialized)))return;e.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(e.matchedTracks.map((async t=>[t.configuration.trackId,await ue(e,t)])))))}catch(t){console.error(t),(0,c.getSession)(e).notifyError(`${t}`,t)}})))},menuItems:()=>[...e.views.map(((e,t)=>[t,e.menuItems()])).map((e=>({label:`Row ${e[0]+1} view menu`,subMenu:e[1]}))),{label:"Reverse view order",onClick:()=>{e.reverseViewOrder()}},{label:"Show intra-view links",type:"checkbox",checked:e.showIntraviewLinks,onClick:()=>{e.toggleIntraviewLinks()}},{label:"Allow clicking alignment squiggles?",type:"checkbox",checked:e.interactToggled,onClick:()=>{e.toggleInteract()}},{label:"Link views",type:"checkbox",icon:se.A,checked:e.linkViews,onClick:()=>{e.toggleLinkViews()}},{label:"Export SVG",icon:ie.A,onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[ce,{model:e,handleClose:t}]))}}]})))}class me extends a.A{name="BreakpointSplitViewPlugin";install(e){!function(e){e.addViewType((()=>new ne({name:"BreakpointSplitView",displayName:"Breakpoint split view",stateModel:pe(e),ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(5727),r.e(7348)]).then(r.bind(r,67348))))})))}(e),function(e){e.addWidgetType((()=>new Q.WidgetType({name:"BreakpointAlignmentsWidget",heading:"Breakpoint feature details",configSchema:Z,stateModel:ee,ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(8565),r.e(5676),r.e(3011),r.e(6157),r.e(6683),r.e(2627),r.e(8984),r.e(5677)]).then(r.bind(r,90439))))})))}(e)}configure(){}}var ge=r(14349),he=r(59099);const fe=(0,i.ConfigurationSchema)("PAFAdapter",{assemblyNames:{type:"stringArray",defaultValue:[],description:"Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second"},targetAssembly:{type:"string",defaultValue:"",description:"Alternative to assemblyNames: the target assembly name"},queryAssembly:{type:"string",defaultValue:"",description:"Alternative to assemblyNames: the query assembly name"},pafLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/file.paf",locationType:"UriLocation"}}},{explicitlyTyped:!0}),ye=(0,i.ConfigurationSchema)("PairwiseIndexedPAFAdapter",{assemblyNames:{type:"stringArray",defaultValue:[],description:"Array of assembly names to use for this file. 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n=this.getCoords(t,r);if(n){const[t,r,a,o]=n,i=(0,c.getSession)(e),s=Ie.create({...(0,d.getSnapshot)(e.hview),minimumBlockWidth:0,interRegionPaddingWidth:0}),l=Ie.create({...(0,d.getSnapshot)(e.vview),minimumBlockWidth:0,interRegionPaddingWidth:0});s.setVolatileWidth(e.hview.width),l.setVolatileWidth(e.vview.width),s.moveTo(t,r),l.moveTo(o,a),s.zoomTo(s.bpPerPx/(e.width/e.hview.width),0),l.zoomTo(l.bpPerPx/(e.width/e.vview.width),0);const u=e.tracks.map((e=>e.configuration.displays.find((e=>"LinearSyntenyDisplay"===e.type)))).filter((e=>!!e)).map((e=>{const t=(0,d.getParent)(e,2);return{type:t.type,configuration:t,displays:[{type:e.type,configuration:e}]}})),{id:p,...m}=(0,d.getSnapshot)(s),{id:g,...h}=(0,d.getSnapshot)(l),f={type:"LinearSyntenyView",views:[{type:"LinearGenomeView",tracks:[],hideHeader:!0,...m},{type:"LinearGenomeView",tracks:[],hideHeader:!0,...h}],tracks:u};i.addView("LinearSyntenyView",f)}}}))).actions((e=>({async exportSvg(t={}){const{renderToSvg:n}=await r.e(1266).then(r.bind(r,11266)),a=await n(e,t),o=new Blob([a],{type:"image/svg+xml"});(0,oe.saveAs)(o,t.filename||"image.svg")},beforeDestroy(){const t=(0,c.getSession)(e);for(const r in e.assemblyNames)t.removeTemporaryAssembly?.(r)},afterAttach(){(0,d.addDisposer)(e,(0,ae.autorun)((()=>{const{showPanButtons:t,wheelMode:r,cursorMode:n}=e;var a;"undefined"!=typeof localStorage&&(localStorage.setItem("dotplot-showPanbuttons",(a=t,JSON.stringify(a))),localStorage.setItem("dotplot-cursorMode",n),localStorage.setItem("dotplot-wheelMode",r))}))),(0,d.addDisposer)(e,(0,ae.autorun)((()=>{const t=(0,c.getSession)(e);if(void 0===e.volatileWidth||!e.assembliesInitialized)return;if(e.hview.displayedRegions.length>0&&e.vview.displayedRegions.length>0)return;const r=[e.hview,e.vview];(0,ae.transaction)((()=>{e.assemblyNames.forEach(((e,n)=>{const a=t.assemblyManager.get(e);r[n].setDisplayedRegions(a?.regions||[])})),e.showAllRegions()}))}),{delay:1e3})),(0,d.addDisposer)(e,(0,ae.autorun)((function(){if(void 0===e.volatileWidth)return;const{vview:t,hview:r,viewHeight:n,viewWidth:a}=e,o=t.dynamicBlocks.contentBlocks,i=r.dynamicBlocks.contentBlocks,s=r.offsetPx,l=t.offsetPx,c=(0,Le.rQ)(o,n,l),d=(0,Le.rQ)(i,a,s),u=ze(i,t.bpPerPx,d),p=ze(o,r.bpPerPx,c);e.setBorderY(Math.max(u+40,50)),e.setBorderX(Math.max(p+40,50))})))},squareView(){const{hview:t,vview:r}=e,n=(t.bpPerPx+r.bpPerPx)/2,a=t.pxToBp(t.width/2),o=r.pxToBp(r.width/2);t.setBpPerPx(n),t.centerAt(a.coord,a.refName,a.index),r.setBpPerPx(n),r.centerAt(o.coord,o.refName,o.index)},squareViewProportional(){const{hview:t,vview:r}=e,n=t.width/r.width,a=(t.bpPerPx+r.bpPerPx)/2,o=t.pxToBp(t.width/2),i=r.pxToBp(r.width/2);t.setBpPerPx(a/n),t.centerAt(o.coord,o.refName,o.index),r.setBpPerPx(a),r.centerAt(i.coord,i.refName,i.index)}}))).views((e=>({menuItems(){const t=(0,c.getSession)(e);return[{label:"Return to import form",onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[Be,{model:e,handleClose:t}]))},icon:Me.A},{label:"Square view - same bp per pixel",onClick:()=>{e.squareView()}},{label:"Rectangular view - same total bp",onClick:()=>{e.squareView()}},{label:"Show all regions",onClick:()=>{e.showAllRegions()}},{label:"Export SVG",icon:ie.A,onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[De,{model:e,handleClose:t}]))}},...(0,c.isSessionModelWithWidgets)(t)?[{label:"Open track selector",onClick:e.activateTrackSelector,icon:Pe.xU}]:[]]},get error(){return e.volatileError||e.assemblyErrors}})))),ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(5515),r.e(3474)]).then(r.bind(r,63474))))});var t}))}(e),(t=e).addDisplayType((()=>{const e=function(e){return(0,i.ConfigurationSchema)("DotplotDisplay",{renderer:d.types.optional(e.pluggableConfigSchemaType("renderer"),{type:"DotplotRenderer"})},{explicitIdentifier:"displayId",explicitlyTyped:!0})}(t);return new Oe.A({name:"DotplotDisplay",displayName:"Dotplot display",configSchema:e,stateModel:Qe(e),trackType:"SyntenyTrack",viewType:"DotplotView",ReactComponent:tt})})),function(e){e.addRendererType((()=>new at({name:"DotplotRenderer",configSchema:ot,ReactComponent:rt,pluginManager:e})))}(e),function(e){e.addToExtensionPoint("LaunchView-DotplotView",(async({session:e,views:t,tracks:r=[]})=>{try{const n=e.addView("DotplotView",{}),a=t.map((e=>e.assembly));(0,ae.transaction)((()=>{n.setViews([{bpPerPx:.1,offsetPx:0},{bpPerPx:.1,offsetPx:0}]),n.setAssemblyNames(a[0],a[1])}));const o=[];if(r.forEach((e=>{!function(e,t,r){try{e.showTrack(t)}catch(e){if(!/Could not resolve identifier/.exec(`${e}`))throw e;r.push(t)}}(n,e,o)})),o.length)throw new Error(`Could not resolve identifiers: ${o.join(",")}`)}catch(t){throw e.notifyError(`${t}`,t),t}}))}(e),function(e){e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearPileupDisplay"===e.name){const{stateModel:t}=e,r=t.extend((e=>{const t=e.contextMenuItems;return{views:{contextMenuItems(){const r=e.contextMenuFeature;return[...t(),...r?[{label:"Dotplot of read vs ref",icon:lt.A,onClick:()=>{!function(e,t){const r=(0,c.getSession)(t);try{const n=e.get("CIGAR"),a=dt(n,1),o=e.get("flags"),s=e.get("strand"),l=e.get("name"),d=`${l}_assembly_${Date.now()}`,{parentTrack:u}=t,[p]=(0,i.getConf)(u,"assemblyNames"),m=[p,d],g=`track-${Date.now()}`,h=`${l}_vs_${p}`,f=ut(e,"SA")||"",y=ct(f,e.id(),s,l,!0),b=e.toJSON();b.strand=1,b.mate={refName:l,start:a,end:a+mt(n)};const w=pt(2048&o?y[0].CIGAR:n),v=[b,...y];v.sort(((e,t)=>e.clipPos-t.clipPos));const C=v.reduce(((e,t)=>e+t.end-t.start),0);r.addView("DotplotView",{type:"DotplotView",hview:{offsetPx:0,bpPerPx:C/800,displayedRegions:(0,c.gatherOverlaps)(v.map(((e,t)=>{const{start:r,end:n,refName:a}=e;return{start:r,end:n,refName:a,index:t,assemblyName:p}})))},vview:{offsetPx:0,bpPerPx:w/400,minimumBlockWidth:0,interRegionPaddingWidth:0,displayedRegions:[{assemblyName:d,start:0,end:w,refName:l}]},viewTrackConfigs:[{type:"SyntenyTrack",assemblyNames:m,adapter:{type:"FromConfigAdapter",features:v},trackId:g,name:h}],assemblyNames:m,tracks:[{configuration:g,type:"SyntenyTrack",displays:[{type:"DotplotDisplay",configuration:`${g}-DotplotDisplay`}]}],displayName:`${l} vs ${p}`})}catch(e){console.error(e),r.notifyError(`${e}`,e)}}(r,e)}}]:[]]}}}}));e.stateModel=r}return e}))}(e),e.addRpcMethod((()=>new st(e)))}configure(e){(0,c.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Dotplot view",icon:xe.A,onClick:e=>{e.addView("DotplotView",{})}})}}const ht=(0,i.ConfigurationSchema)("GtfAdapter",{gtfLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.gtf",locationType:"UriLocation"}}},{explicitlyTyped:!0});class ft extends a.A{name="GTFPlugin";install(e){e.addAdapterType((()=>new $.A({name:"GtfAdapter",displayName:"GTF adapter",configSchema:ht,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(4499),r.e(1503)]).then(r.bind(r,61503)).then((e=>e.default))}))),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="GtfAdapter",o=(0,X.getFileName)(t),i={type:a,gtfLocation:t};return/\.gtf(\.gz)?$/i.test(o)&&!n||n===a?i:e(t,r,n)}))}}const yt=(0,i.ConfigurationSchema)("Gff3TabixAdapter",{gffGzLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.gff.gz",locationType:"UriLocation"}},index:(0,i.ConfigurationSchema)("Gff3TabixIndex",{indexType:{model:d.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.gff.gz.tbi",locationType:"UriLocation"}}}),dontRedispatch:{type:"stringArray",defaultValue:["chromosome","region","contig"]}},{explicitlyTyped:!0}),bt=(0,i.ConfigurationSchema)("Gff3Adapter",{gffLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.gff",locationType:"UriLocation"}}},{explicitlyTyped:!0});class wt extends a.A{name="GFF3Plugin";install(e){!function(e){e.addAdapterType((()=>new Q.AdapterType({name:"Gff3TabixAdapter",displayName:"GFF3 tabix adapter",configSchema:yt,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(8120),r.e(2645),r.e(7409)]).then(r.bind(r,27409)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new Q.AdapterType({name:"Gff3Adapter",displayName:"GFF3 adapter",configSchema:bt,getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(4499),r.e(2645),r.e(7809)]).then(r.bind(r,37809)).then((e=>e.default))})))}(e),function(e){e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="Gff3TabixAdapter",o=(0,X.getFileName)(t),i=r&&(0,X.getFileName)(r);return/\.gff3?\.b?gz$/i.test(o)||n===a?{type:a,bamLocation:t,gffGzLocation:t,index:{location:r||(0,X.makeIndex)(t,".tbi"),indexType:(0,X.makeIndexType)(i,"CSI","TBI")}}:e(t,r,n)})),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="Gff3Adapter",o=(0,X.getFileName)(t),i={type:a,gffLocation:t};return/\.gff3?$/i.test(o)&&!n||n===a?i:e(t,r,n)}))}(e)}}const vt=d.types.model("Job",{name:d.types.string,statusMessage:d.types.maybe(d.types.string),progressPct:d.types.number}).volatile((()=>({cancelCallback(){}}))).actions((e=>({setCancelCallback(t){e.cancelCallback=t},setStatusMessage(t){e.statusMessage=t},setProgressPct(t){e.progressPct=t}}))),Ct=(0,i.ConfigurationSchema)("JobsListWidget",{});class St extends a.A{name="JobsManagementPlugin";install(e){!function(e){e.addWidgetType((()=>new Q.WidgetType({name:"JobsListWidget",heading:"Jobs list",configSchema:Ct,stateModel:d.types.model("JobsListModel",{id:K.ElementId,type:d.types.literal("JobsListWidget"),jobs:d.types.array(vt),finished:d.types.array(vt),queued:d.types.array(vt),aborted:d.types.array(vt)}).actions((e=>({addJob(t){const{cancelCallback:r}=t,n=e.jobs.push(t),a=e.jobs[n-1];return a.setCancelCallback(r),a},removeJob(t){const r=e.jobs.findIndex((e=>e.name===t)),n=e.jobs[r];return e.jobs.splice(r,1),n},addFinishedJob:t=>(e.finished.push(t),e.finished),addQueuedJob:t=>(e.queued.push(t),e.finished),addAbortedJob:t=>(e.aborted.push(t),e.aborted),removeQueuedJob(t){const r=e.queued.findIndex((e=>e.name===t)),n=e.queued[r];return e.queued.splice(r,1),n},updateJobStatusMessage(t,r){const n=e.jobs.find((e=>e.name===t));if(!n)throw new Error(`No job found with name ${t}`);n.setStatusMessage(r)},updateJobProgressPct(t,r){const n=e.jobs.find((e=>e.name===t));if(!n)throw new Error(`No job found with name ${t}`);n.setProgressPct(r)}}))),ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(3011),r.e(9168)]).then(r.bind(r,29168))))})))}(e)}configure(e){(0,c.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToMenu("Tools",{label:"Jobs list",icon:Pe.jT,onClick:e=>{if((0,c.isSessionModelWithWidgets)(e)){const{widgets:t}=e;let r=t.get("JobsList");r||(r=e.addWidget("JobsListWidget","JobsList")),e.showWidget(r)}}})}}const kt=(0,i.ConfigurationSchema)("NCListAdapter",{rootUrlTemplate:{type:"fileLocation",defaultValue:{uri:"/path/to/my/{refseq}/trackData.json",locationType:"UriLocation"}},refNames:{type:"stringArray",defaultValue:[],description:"List of refNames used by the NCList used for aliasing"}},{explicitlyTyped:!0});var Tt=r(8024);const xt=(0,i.ConfigurationSchema)("JBrowse1TextSearchAdapter",{namesIndexLocation:{type:"fileLocation",defaultValue:{uri:"/volvox/names",locationType:"UriLocation"},description:"the location of the JBrowse1 names index data directory"},tracks:{type:"stringArray",defaultValue:[],description:"List of tracks covered by text search adapter"},assemblyNames:{type:"stringArray",defaultValue:[],description:"List of assemblies covered by text search adapter"}},{explicitlyTyped:!0,explicitIdentifier:"textSearchAdapterId"});var At=r(91612);const Pt=(0,i.ConfigurationSchema)("JBrowse1Connection",{dataDirLocation:{type:"fileLocation",defaultValue:{uri:"http://mysite.com/jbrowse/data/",locationType:"UriLocation"},description:"the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/"},assemblyNames:{description:"name of the assembly the connection belongs to, should be a single entry",type:"stringArray",defaultValue:[]}},{baseConfiguration:s.baseConnectionConfig});function Mt(e){return d.types.compose("JBrowse1Connection",(0,s.BaseConnectionModelFactory)(e),d.types.model({configuration:(0,i.ConfigurationReference)(Pt),type:d.types.literal("JBrowse1Connection")})).actions((e=>({async connect(){const t=(0,c.getSession)(e);try{const n=(0,i.getConf)(e,"dataDirLocation"),{fetchJb1:a}=await r.e(7911).then(r.bind(r,77911)),{convertTrackConfig:o}=await r.e(5998).then(r.bind(r,55998)),s=await a(n),l=(0,i.getConf)(e,"assemblyNames")[0];if(!l)throw new Error("assembly name required for JBrowse 1 connection");const c=t.assemblies.find((e=>(0,i.readConfObject)(e,"name")===l));if(!c)throw new Error(`Assembly "${l}" not found`);const d=(0,i.readConfObject)(c,["sequence","adapter"]),u=s.tracks?.map((e=>({...o(e,s.dataRoot||"",d),assemblyNames:[l]})));e.setTrackConfs(u)}catch(r){console.error(r),t.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${e.name}". Please make sure you have entered a valid location. The error that was thrown is: "${r}"`,r),t.breakConnection?.(e.configuration)}}})))}class Et extends a.A{name="LegacyJBrowsePlugin";install(e){!function(e){e.addAdapterType((()=>new Q.AdapterType({name:"NCListAdapter",displayName:"NCList adapter",configSchema:kt,getAdapterClass:()=>r.e(3525).then(r.bind(r,33525)).then((e=>e.default))})))}(e),function(e){e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="NCListAdapter",o=(0,X.getFileName)(t);return/trackData.jsonz?$/i.test(o)||n===a?{type:a,rootUrlTemplate:t}:e(t,r,n)}))}(e),function(e){e.addTextSearchAdapterType((()=>new Tt.A({name:"JBrowse1TextSearchAdapter",configSchema:xt,description:"A JBrowse 1 text search adapter",getAdapterClass:()=>r.e(8797).then(r.bind(r,58797)).then((e=>e.default))})))}(e),function(e){e.addConnectionType((()=>new At.A({name:"JBrowse1Connection",configSchema:Pt,stateModel:Mt(e),displayName:"JBrowse 1 Data",description:"A JBrowse 1 data directory",url:"//jbrowse.org/"})))}(e)}}var Rt=r(20529),It=r(24250);const Nt=function(e){return(0,i.ConfigurationSchema)("LinearComparativeDisplay",{},{explicitlyTyped:!0,explicitIdentifier:"displayId"})};function Ft(e){const{rpcManager:t}=(0,c.getSession)(e),r=e;(0,i.readConfObject)(e.configuration);const{adapterConfig:n}=e,a=(0,c.getContainingView)(e),o=(0,X.getRpcSessionId)(e);return(0,d.getSnapshot)(a),a.initialized?{rpcManager:t,renderProps:{...r.renderProps(),view:a,adapterConfig:n,sessionId:o,timeout:1e6,self:e}}:void 0}async function Lt(e){if(!e)return;const{rpcManager:t,renderProps:r}=e,{adapterConfig:n}=r,a=r.view.views[0],o=await t.call("getFeats","CoreGetFeatures",{regions:a.staticBlocks.contentBlocks,sessionId:"getFeats",adapterConfig:n});return{features:(0,c.dedupe)(o,(e=>e.id()))}}const Dt=function(e){return d.types.compose("LinearComparativeDisplay",s.BaseDisplay,d.types.model({type:d.types.literal("LinearComparativeDisplay"),configuration:(0,i.ConfigurationReference)(e),height:100})).volatile((()=>({renderInProgress:void 0,features:void 0,message:void 0}))).views((e=>({renderProps:()=>({rpcDriverName:e.rpcDriverName,displayModel:e,highResolutionScaling:2})}))).actions((e=>{let t;return{setLoading(r){e.message=void 0,e.error=void 0,t=r},setMessage(r){t&&!t.signal.aborted&&t.abort(),e.message=r,e.error=void 0,t=void 0},setRendered(r){if(!r)return;const{features:n}=r,a=e.features||[],o=new Set(a.map((e=>e.id()))),i=new Set(n.map((e=>e.id())));let s=!1,l=!1;for(const e of n)if(!o.has(e.id())){s=!0;break}for(const e of a)if(!i.has(e.id())){l=!0;break}e.message=void 0,e.error=void 0,t=void 0,(s||l||!e.features)&&(e.features=n)},setError(r){console.error(r),t&&!t.signal.aborted&&t.abort(),e.message=void 0,e.error=r,t=void 0}}})).actions((e=>({afterAttach(){(0,c.makeAbortableReaction)(e,Ft,Lt,{name:`${e.type} ${e.id} rendering`,delay:1e3,fireImmediately:!0},e.setLoading,e.setRendered,e.setError)}})))},Bt=(0,w.lazy)((()=>Promise.resolve().then(r.bind(r,87686)))),Vt=function(e){return d.types.compose("LinearComparativeView",Ae.A,d.types.model({id:K.ElementId,type:d.types.literal("LinearComparativeView"),trackSelectorType:"hierarchical",showIntraviewLinks:!0,interactToggled:!1,middleComparativeHeight:100,tracks:d.types.array(e.pluggableMstType("track","stateModel")),views:d.types.array(e.getViewType("LinearGenomeView").stateModel),viewTrackConfigs:d.types.array(e.pluggableConfigSchemaType("track"))})).volatile((()=>({width:void 0}))).views((e=>({get highResolutionScaling(){return 2},get initialized(){return void 0!==e.width&&e.views.length>0&&e.views.every((e=>e.initialized))},get refNames(){return e.views.map((e=>[...new Set(e.staticBlocks.map((e=>e.refName)))]))},get assemblyNames(){return[...new Set(e.views.flatMap((e=>e.assemblyNames)))]}}))).actions((t=>({beforeDestroy(){const e=(0,c.getSession)(t);for(const r of t.assemblyNames)e.removeTemporaryAssembly?.(r)},onSubviewAction(e,r,n){t.views.forEach((t=>{(0,d.getPath)(t).endsWith(r)||t[e](n?.[0])}))},setWidth(e){t.width=e},setViews(e){t.views=(0,d.cast)(e)},removeView(e){t.views.remove(e)},setMiddleComparativeHeight:e=>(t.middleComparativeHeight=e,t.middleComparativeHeight),activateTrackSelector(){if("hierarchical"!==t.trackSelectorType)throw new Error(`invalid track selector type ${t.trackSelectorType}`);{const e=(0,c.getSession)(t);if((0,c.isSessionModelWithWidgets)(e)){const r=e.addWidget("HierarchicalTrackSelectorWidget","hierarchicalTrackSelector",{view:t});return e.showWidget(r),r}}},toggleTrack(e){return!this.hideTrack(e)&&(this.showTrack(e),!0)},showTrack(r,n={}){const a=e.pluggableConfigSchemaType("track"),o=(0,d.resolveIdentifier)(a,(0,d.getRoot)(t),r);if(!o)throw new Error(`track not found ${r}`);const i=e.getTrackType(o.type);if(!i)throw new Error(`unknown track type ${o.type}`);const s=e.getViewType(t.type),l=new Set(s.displayTypes.map((e=>e.name))),c=o.displays.find((e=>l.has(e.type)));if(!c)throw new Error(`could not find a compatible display for view type ${t.type}`);t.tracks.push(i.stateModel.create({...n,type:o.type,configuration:o,displays:[{type:c.type,configuration:c}]}))},hideTrack(r){const n=e.pluggableConfigSchemaType("track"),a=(0,d.resolveIdentifier)(n,(0,d.getRoot)(t),r),o=t.tracks.filter((e=>e.configuration===a));return(0,ae.transaction)((()=>{o.forEach((e=>t.tracks.remove(e)))})),o.length},squareView(){const e=(0,c.avg)(t.views.map((e=>e.bpPerPx)));t.views.forEach((t=>{const r=t.pxToBp(t.width/2);t.setNewView(e,t.offsetPx),r.refName&&t.centerAt(r.coord,r.refName,r.index)}))},clearView(){t.views=(0,d.cast)([]),t.tracks=(0,d.cast)([])}}))).views((()=>({headerMenuItems:()=>[]}))).views((e=>({menuItems:()=>[...e.views.map(((e,t)=>[t,e.menuItems()])).map((e=>({label:`View ${e[0]+1} Menu`,subMenu:e[1]}))),{label:"Return to import form",onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[Bt,{model:e,handleClose:t}]))},icon:Me.A},{label:"Open track selector",onClick:e.activateTrackSelector,icon:Pe.xU}],rubberBandMenuItems:()=>[{label:"Zoom to region(s)",onClick:()=>{e.views.forEach((e=>{const{leftOffset:t,rightOffset:r}=e;t&&r&&e.moveTo(t,r)}))}}]}))).actions((e=>({afterAttach(){(0,d.addDisposer)(e,(0,ae.autorun)((()=>{e.width&&e.views.forEach((t=>{t.setWidth(e.width)}))})))}})))},zt=function(e){return d.types.compose("LinearSyntenyDisplay",Dt(e),d.types.model({type:d.types.literal("LinearSyntenyDisplay"),configuration:(0,i.ConfigurationReference)(e)})).volatile((()=>({mainCanvas:null,clickMapCanvas:null,cigarClickMapCanvas:null,mouseoverCanvas:null,featPositions:[],mouseoverId:void 0,clickId:void 0,cigarMouseoverId:-1}))).actions((e=>({setFeatPositions(t){e.featPositions=t},setMainCanvasRef(t){e.mainCanvas=t},setClickMapCanvasRef(t){e.clickMapCanvas=t},setCigarClickMapCanvasRef(t){e.cigarClickMapCanvas=t},setMouseoverCanvasRef(t){e.mouseoverCanvas=t},setMouseoverId(t){e.mouseoverId=t},setCigarMouseoverId(t){e.cigarMouseoverId=t},setClickId(t){e.clickId=t}}))).views((e=>({get adapterConfig(){return{name:e.parentTrack.configuration.adapter.type,assemblyNames:(0,i.getConf)(e,"assemblyNames"),...(0,i.getConf)(e.parentTrack,"adapter")}},get trackIds(){return(0,i.getConf)(e,"trackIds")},get numFeats(){return e.featPositions.length},get ready(){return this.numFeats>0},get featMap(){return Object.fromEntries(e.featPositions.map((e=>[e.f.id(),e])))}}))).actions((e=>({afterAttach(){(async()=>{try{const{doAfterAttach:t}=await r.e(8856).then(r.bind(r,28856));t(e)}catch(t){console.error(t),e.setError(t)}})()}})))},Ot=(0,w.lazy)((()=>r.e(5682).then(r.bind(r,33301))));var Ht=r(52521),jt=r(1633);function Wt(e){return w.createElement(F.A,e,w.createElement("path",{fill:"currentColor",d:"M16.5,21C13.5,21 12.31,16.76 11.05,12.28C10.14,9.04 9,5 7.5,5C4.11,5 4,11.93 4,12H2C2,11.63 2.06,3 7.5,3C10.5,3 11.71,7.25 12.97,11.74C13.83,14.8 15,19 16.5,19C19.94,19 20.03,12.07 20.03,12H22.03C22.03,12.37 21.97,21 16.5,21Z"}))}const Gt=(0,w.lazy)((()=>r.e(8869).then(r.bind(r,78869))));function $t(e){return d.types.compose("LinearSyntenyView",Vt(e),d.types.model({type:d.types.literal("LinearSyntenyView"),drawCIGAR:!0,drawCurves:!1})).actions((e=>({toggleCurves(){e.drawCurves=!e.drawCurves},toggleCIGAR(){e.drawCIGAR=!e.drawCIGAR},showAllRegions(){(0,ae.transaction)((()=>{e.views.forEach((e=>{e.showAllRegionsInAssembly()}))}))}}))).actions((e=>({async exportSvg(t){const{renderToSvg:n}=await r.e(9658).then(r.bind(r,69658)),a=await n(e,t),o=new Blob([a],{type:"image/svg+xml"});(0,oe.saveAs)(o,t.filename||"image.svg")}}))).views((e=>{const t=e.headerMenuItems,r=e.menuItems;return{headerMenuItems:()=>[...t(),{label:"Square view",onClick:e.squareView,description:"Makes both views use the same zoom level, adjusting to the average of each",icon:Ht.A},{label:"Show all regions",onClick:e.showAllRegions,description:"Show entire genome assemblies",icon:jt.A},{label:"Draw CIGAR",onClick:e.toggleCIGAR,checked:e.drawCIGAR,type:"checkbox",description:"Draws per-base CIGAR level alignments"},{label:"Use curved lines",type:"checkbox",checked:e.drawCurves,onClick:e.toggleCurves,icon:Wt},{label:"Export SVG",icon:ie.A,onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[Gt,{model:e,handleClose:t}]))}}],menuItems:()=>[...r(),{label:"Export SVG",icon:ie.A,onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[Gt,{model:e,handleClose:t}]))}}]}}))}function qt(e,t,r){try{e.showTrack(t)}catch(e){if(!/Could not resolve identifier/.exec(`${e}`))throw e;r.push(t)}}var _t=r(58273);const Ut=(0,w.lazy)((()=>r.e(3416).then(r.bind(r,3416))));class Jt extends a.A{name="LinearComparativeViewPlugin";install(e){!function(e){e.addViewType((()=>new te.A({name:"LinearComparativeView",displayName:"Linear comparative view",stateModel:Vt(e),ReactComponent:(0,w.lazy)((()=>r.e(8876).then(r.bind(r,98876))))})))}(e),function(e){e.addViewType((()=>new te.A({name:"LinearSyntenyView",displayName:"Linear synteny view",stateModel:$t(e),ReactComponent:(0,w.lazy)((()=>r.e(3795).then(r.bind(r,13795))))})))}(e),function(e){e.addDisplayType((()=>{const e=Nt();return new Oe.A({name:"LinearComparativeDisplay",configSchema:e,stateModel:Dt(e),trackType:"SyntenyTrack",viewType:"LinearComparativeView",ReactComponent:()=>null})}))}(e),function(e){e.addDisplayType((()=>{const e=(0,i.ConfigurationSchema)("LinearSyntenyDisplay",{trackIds:{type:"stringArray",defaultValue:[]},middle:{type:"boolean",defaultValue:!0}},{baseConfiguration:Nt(),explicitlyTyped:!0});return new Oe.A({name:"LinearSyntenyDisplay",configSchema:e,stateModel:zt(e),trackType:"SyntenyTrack",viewType:"LinearSyntenyView",ReactComponent:(0,w.lazy)((()=>r.e(4753).then(r.bind(r,44753))))})}))}(e),function(e){e.addDisplayType((()=>{const t=function(e){return(0,i.ConfigurationSchema)("LGVSyntenyDisplay",{},{baseConfiguration:(0,n.ww)(e),explicitlyTyped:!0})}(e),r=(a=t,d.types.compose("LGVSyntenyDisplay",(0,n.N5)(a),d.types.model({type:d.types.literal("LGVSyntenyDisplay"),configuration:(0,i.ConfigurationReference)(a)})).views((e=>{const t=e.contextMenuItems;return{contextMenuItems(){const r=e.contextMenuFeature;return[...t(),...r?[{label:"Open synteny view for this position",onClick:()=>{(0,c.getSession)(e).queueDialog((t=>[Ot,{model:e,handleClose:t,feature:r}]))}}]:[]]}}})).views((e=>{const{trackMenuItems:t,colorSchemeSubMenuItems:r}=e;return{trackMenuItems:()=>[...t(),{label:"Color scheme",subMenu:[...r()]}]}})).actions((e=>({afterCreate(){e.colorBy?e.setColorScheme({...e.colorBy}):e.setColorScheme({type:"strand"})}}))));var a;return new Oe.A({name:"LGVSyntenyDisplay",configSchema:t,stateModel:r,trackType:"SyntenyTrack",viewType:"LinearGenomeView",ReactComponent:Rt.GQ})}))}(e),function(e){e.addToExtensionPoint("LaunchView-LinearSyntenyView",(async({session:e,views:t,tracks:r=[]})=>{try{const{assemblyManager:n}=e,a=e.addView("LinearSyntenyView",{});await(0,ae.when)((()=>!!a.width)),a.setViews(await Promise.all(t.map((async e=>{const t=await n.waitForAssembly(e.assembly);if(!t)throw new Error(`Assembly ${e.assembly} failed to load`);return{type:"LinearGenomeView",bpPerPx:1,offsetPx:0,hideHeader:!0,displayedRegions:t.regions}})))),await Promise.all(a.views.map((e=>(0,ae.when)((()=>e.initialized)))));const o=[];if(await Promise.all(t.map((async(e,t)=>{const r=a.views[t],{assembly:i,loc:s,tracks:l=[]}=e,c=await n.waitForAssembly(i);if(!c)throw new Error(`Assembly ${e.assembly} failed to load`);await r.navToSearchString({input:s,assembly:c}),l.forEach((e=>{qt(r,e,o)}))}))),r.forEach((e=>{qt(a,e,o)})),o.length)throw new Error(`Could not resolve identifiers: ${o.join(",")}`)}catch(t){throw e.notifyError(`${t}`,t),t}}))}(e),function(e){e.addTrackType((()=>{const t=(e=>(0,i.ConfigurationSchema)("SyntenyTrack",{},{baseConfiguration:(0,s.createBaseTrackConfig)(e)}))(e);return new _t.A({name:"SyntenyTrack",configSchema:t,stateModel:(0,s.createBaseTrackModel)(e,"SyntenyTrack",t)})}))}(e),e.addToExtensionPoint("Core-extendPluggableElement",(e=>("LinearPileupDisplay"!==e.name||(e.stateModel=e.stateModel.extend((e=>{const t=e.contextMenuItems;return{views:{contextMenuItems(){const r=e.contextMenuFeature,n=(0,c.getContainingTrack)(e);return[...t(),...r?[{label:"Linear read vs ref",icon:lt.A,onClick:()=>{(0,c.getSession)(e).queueDialog((e=>[Ut,{track:n,feature:r,handleClose:e}]))}}]:[]]}}}}))),e)))}configure(e){(0,c.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Linear synteny view",icon:It.A,onClick:e=>{e.addView("LinearSyntenyView",{})}})}}function Xt(e){return d.types.compose("LinearLollipopDisplay",Rt.Lr,d.types.model({type:d.types.literal("LinearLollipopDisplay"),configuration:(0,i.ConfigurationReference)(e)})).views((e=>{const{renderProps:t}=e;return{get blockType(){return"dynamicBlocks"},get renderDelay(){return 500},renderProps:()=>({...t(),rpcDriverName:e.rpcDriverName,config:e.configuration.renderer}),get rendererTypeName(){return e.configuration.renderer.type}}}))}var Yt=r(98111),Kt=r(2265),Qt=r(32595);class Zt{totalHeight=0;constructor({width:e}){if(!e)throw new Error("width required to make a new FloatingLayout");this.width=e}items=[];layout=new Map;layoutDirty=!1;add(e,t,r,n,a){this.items.push({uniqueId:e,anchorLocation:t,width:r,height:n,data:a}),this.layoutDirty=!0}getLayout(e){if(!this.layoutDirty)return this.layout;if(!e)throw new Error("configuration object required");const t=(0,i.readConfObject)(e,"minStickLength"),r=this.items.sort(((e,t)=>e.data.score-t.data.score));let n=0;const a=new Array(r.length);for(let e=0;e<r.length;e+=1){const o=r[e],{anchorLocation:i,width:s,height:l}=o,c=i-s/2,d=c+s;let u=t,p=u+l;for(let t=0;t<e;t+=1){const[,e]=a[t],{x:r,y:n,width:o,height:i}=e,s=r+o,m=n+i;(0,Qt.R6)(r,s,c,d)&&(0,Qt.R6)(n,m,u,p)&&(u=m,p=u+l,t=-1)}a[e]=[o.uniqueId,{...o,x:c,y:u}],p>n&&(n=p)}return this.totalHeight=n,this.layout=new Map(a),this.layoutDirty=!1,this.layout}getTotalHeight(){if(this.layoutDirty)throw new Error("getTotalHeight does not work when the layout is dirty.");return this.totalHeight}serializeRegion(){return this.toJSON()}toJSON(){if(this.layoutDirty)throw new Error("toJSON does not work when the layout is dirty.");return{pairs:[...this.getLayout()],totalHeight:this.getTotalHeight()}}static fromJSON(){throw new Error("not supported")}}class er{constructor({pairs:e,totalHeight:t}){this.layout=new Map(e),this.totalHeight=t}add(e){if(!this.layout.has(e))throw new Error(`layout error, precomputed layout is missing ${e}`)}getLayout(){return this.layout}getTotalHeight(){return this.totalHeight}static fromJSON(e){return new er(e)}}class tr extends Yt.LayoutSession{makeLayout(){const{end:e,start:t}=this.regions[0],r=(e-t)/this.bpPerPx;return new Kt.A(Zt,{width:r})}layoutIsValid(){return!1}}class rr extends Yt.default{createSession(e){return new tr(e)}deserializeLayoutInClient(e){return new er(e)}}const nr=(0,i.ConfigurationSchema)("LollipopRenderer",{strokeColor:{type:"color",description:"the outer color of each lollipop",defaultValue:"green",contextVariable:["feature"]},innerColor:{type:"color",description:"the inner color of each lollipop",defaultValue:"#7fc75f",contextVariable:["feature"]},strokeWidth:{type:"number",description:"width of the stroked border",defaultValue:4,contextVariable:["feature"]},radius:{type:"number",description:"radius in pixels of each lollipop body",defaultValue:"jexl:sqrt(max(3, (get(feature,'score')*10)/3.14))",contextVariable:["feature"]},caption:{type:"string",description:"the tooltip caption displayed when the mouse hovers over a lollipop",defaultValue:"jexl:get(feature,'name')",contextVariable:["feature"]},minStickLength:{type:"number",description:'minimum lollipop "stick" length, in pixels',defaultValue:5},stickColor:{type:"color",description:"color of the lollipop stick",defaultValue:"black",contextVariable:["feature"]},stickWidth:{type:"number",description:"width in pixels of the lollipop stick",defaultValue:2,contextVariable:["feature"]},score:{type:"number",description:'the "score" of each lollipop, displayed as a number in the center of the circle',defaultValue:"jexl:get(feature,'score')",contextVariable:["feature"]}},{explicitlyTyped:!0});class ar extends a.A{name="LollipopPlugin";install(e){!function(e){e.addRendererType((()=>new rr({name:"LollipopRenderer",ReactComponent:(0,w.lazy)((()=>r.e(6861).then(r.bind(r,46861)))),configSchema:nr,pluginManager:e})))}(e),function(e){e.addDisplayType((()=>{const t=function(e){return(0,i.ConfigurationSchema)("LinearLollipopDisplay",{renderer:e.pluggableConfigSchemaType("renderer")},{baseConfiguration:Rt.Ki,explicitlyTyped:!0})}(e);return new Q.DisplayType({name:"LinearLollipopDisplay",configSchema:t,stateModel:Xt(t),trackType:"LollipopTrack",viewType:"LinearGenomeView",ReactComponent:Rt.GQ})}))}(e)}}function or(e){return d.types.compose("LinearArcDisplay",Rt.Lr,d.types.model({type:d.types.literal("LinearArcDisplay"),configuration:(0,i.ConfigurationReference)(e),displayMode:d.types.maybe(d.types.string)})).views((e=>({get blockType(){return"staticBlocks"},get renderDelay(){return 500},get rendererTypeName(){return e.configuration.renderer.type}}))).views((e=>({get displayModeSetting(){return e.displayMode??(0,i.getConf)(e,["renderer","displayMode"])}}))).views((e=>({get rendererConfig(){const t=(0,i.getConf)(e,["renderer"])||{};return e.rendererType.configSchema.create({...t,displayMode:e.displayModeSetting},(0,c.getEnv)(e))}}))).views((e=>{const{renderProps:t}=e;return{renderProps:()=>({...t(),rpcDriverName:e.rpcDriverName,config:e.rendererConfig,height:e.height})}})).actions((e=>({setDisplayMode(t){e.displayMode=t}}))).views((e=>{const t=e.trackMenuItems;return{trackMenuItems:()=>[...t(),{label:"Display mode",subMenu:[{type:"radio",label:"Arcs",onClick:()=>{e.setDisplayMode("arcs")},checked:"arcs"===e.displayMode},{type:"radio",label:"Semi-circles",onClick:()=>{e.setDisplayMode("semicircles")},checked:"semicircles"===e.displayMode}]}]}}))}function ir(e){return d.types.compose("LinearPairedArcDisplay",Q.BaseDisplay,(0,Rt._e)(),(0,Rt.e6)(),d.types.model({type:d.types.literal("LinearPairedArcDisplay"),configuration:(0,i.ConfigurationReference)(e),displayMode:d.types.maybe(d.types.string)})).volatile((()=>({lastDrawnOffsetPx:0,features:void 0,loading:!1,drawn:!0}))).views((e=>({get displayModeSetting(){return e.displayMode??(0,i.getConf)(e,["renderer","displayMode"])}}))).actions((e=>({selectFeature(t){const r=(0,c.getSession)(e);if((0,c.isSessionModelWithWidgets)(r)){const n=r.addWidget("VariantFeatureWidget","variantFeature",{view:(0,c.getContainingView)(e),track:(0,c.getContainingTrack)(e),featureData:t.toJSON()});r.showWidget(n)}(0,c.isSelectionContainer)(r)&&r.setSelection(t)},setLoading(t){e.loading=t},setFeatures(t){e.features=t},setDisplayMode(t){e.displayMode=t}}))).actions((e=>({afterAttach(){(async()=>{try{const{doAfterAttach:t}=await r.e(3497).then(r.bind(r,93497));t(e)}catch(t){console.error(t),e.setError(t)}})()},async renderSvg(t){const{renderArcSvg:n}=await r.e(4345).then(r.bind(r,44345));return n(e,t)}})))}function sr(){return sr=Object.assign?Object.assign.bind():function(e){for(var t=1;t<arguments.length;t++){var r=arguments[t];for(var n in r)({}).hasOwnProperty.call(r,n)&&(e[n]=r[n])}return e},sr.apply(null,arguments)}const lr=(0,w.lazy)((()=>r.e(2241).then(r.bind(r,72241))));function cr({selectedFeatureId:e,region:t,bpPerPx:r,config:n,height:a,feature:o,onFeatureClick:s}){const[l,d]=(0,w.useState)(!1),[u,p]=(0,c.bpSpanPx)(o.get("start"),o.get("end"),t,r),m=o.id(),g=e&&String(e)===String(o.id()),h=g?"red":(0,i.readConfObject)(n,"color",{feature:o}),f=g?"red":"black",y=(0,i.readConfObject)(n,"label",{feature:o}),b=(0,i.readConfObject)(n,"caption",{feature:o}),v=(0,i.readConfObject)(n,"thickness",{feature:o})||2,C=Math.min((0,i.readConfObject)(n,"height",{feature:o})||100,a),S=w.createRef(),k=.5*C*.75+.375*C;return w.createElement("g",null,w.createElement("path",sr({ref:S},(0,c.getStrokeProps)(h),{d:`M ${u} 0 C ${u} ${C}, ${p} ${C}, ${p} 0`,strokeWidth:v,fill:"transparent",onClick:e=>{s(e,m)},onMouseOver:()=>{d(!0)},onMouseLeave:()=>{d(!1)},pointerEvents:"stroke"})),l?w.createElement(w.Suspense,{fallback:null},w.createElement(lr,{contents:b})):null,w.createElement("text",{x:u+(p-u)/2,y:k+3,stroke:"white",strokeWidth:"0.6em"},y),w.createElement("text",{x:u+(p-u)/2,y:k+3,stroke:f},y))}function dr(e,t,r,n){const a=(n-90)*Math.PI/180;return{x:e+r*Math.cos(a),y:t+r*Math.sin(a)}}function ur(e,t,r,n,a){const o=dr(e,t,r,a),i=dr(e,t,r,n),s=a-n<=180?"0":"1";return["M",o.x,o.y,"A",r,r,0,s,0,i.x,i.y].join(" ")}function pr({selectedFeatureId:e,region:t,bpPerPx:r,config:n,onFeatureClick:a,feature:o}){const[s,l]=(0,w.useState)(!1),[d,u]=(0,c.bpSpanPx)(o.get("start"),o.get("end"),t,r),p=o.id(),m=e&&String(e)===String(o.id()),g=m?"red":(0,i.readConfObject)(n,"color",{feature:o}),h=m?"red":"black",f=(0,i.readConfObject)(n,"label",{feature:o}),y=(0,i.readConfObject)(n,"caption",{feature:o}),b=(0,i.readConfObject)(n,"thickness",{feature:o})||2,v=w.createRef(),C=(u-d)/2;return w.createElement("g",null,w.createElement("path",sr({d:ur(d+(u-d)/2,0,(u-d)/2,90,270)},(0,c.getStrokeProps)(g),{strokeWidth:b,fill:"transparent",onClick:e=>{a(e,p)},onMouseOver:()=>{l(!0)},onMouseLeave:()=>{l(!1)},ref:v,pointerEvents:"stroke"})),s?w.createElement(lr,{contents:y}):null,w.createElement("text",{x:d+(u-d)/2,y:C+3,stroke:"white",strokeWidth:"0.6em"},f),w.createElement("text",{x:d+(u-d)/2,y:C+3,stroke:h},f))}function mr({exportSVG:e,width:t,height:r,children:n}){return e?n:w.createElement("svg",{width:t,height:r},n)}const gr=(0,We.observer)((function({features:e,config:t,regions:r,bpPerPx:n,height:a,exportSVG:o,displayModel:s,onFeatureClick:l}){const c=r[0],d=(c.end-c.start)/n,u="semicircles"===(0,i.readConfObject)(t,"displayMode"),{selectedFeatureId:p}=s||{};return w.createElement(mr,{exportSVG:o,width:d,height:a},[...e.values()].map((e=>u?w.createElement(pr,{key:e.id(),config:t,region:c,bpPerPx:n,selectedFeatureId:p,onFeatureClick:l,feature:e}):w.createElement(cr,{key:e.id(),height:a,config:t,region:c,bpPerPx:n,selectedFeatureId:p,onFeatureClick:l,feature:e}))))})),hr=(0,i.ConfigurationSchema)("ArcRenderer",{color:{type:"color",description:"the color of the arcs",defaultValue:"darkblue",contextVariable:["feature"]},thickness:{type:"number",description:"the thickness of the arcs",defaultValue:"jexl:logThickness(feature,'score')",contextVariable:["feature"]},label:{type:"string",description:"the label to appear at the apex of the arcs",defaultValue:"jexl:get(feature,'score')",contextVariable:["feature"]},height:{type:"number",description:"the height of the arcs",defaultValue:"jexl:log10(get(feature,'end')-get(feature,'start'))*50",contextVariable:["feature"]},caption:{type:"string",description:"the caption to appear when hovering over any point on the arcs",defaultValue:"jexl:get(feature,'name')",contextVariable:["feature"]},displayMode:{type:"enum",defaultValue:"arcs",model:d.types.enumeration("DisplayMode",["arcs","semicircles"]),description:"render semi-circles instead of arcs"}},{explicitlyTyped:!0});var fr=r(92880);class yr extends fr.default{}var br=r(40898);class wr extends a.A{name="ArcRenderer";install(e){!function(e){e.addRendererType((()=>new yr({name:"ArcRenderer",ReactComponent:gr,configSchema:hr,pluginManager:e})))}(e),function(e){e.addDisplayType((()=>{const t=function(e){return(0,i.ConfigurationSchema)("LinearArcDisplay",{renderer:d.types.optional(e.pluggableConfigSchemaType("renderer"),{type:"ArcRenderer"})},{baseConfiguration:Rt.Ki,explicitlyTyped:!0})}(e);return new Q.DisplayType({name:"LinearArcDisplay",displayName:"Arc display",configSchema:t,stateModel:or(t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:Rt.GQ})}))}(e),function(e){e.addDisplayType((()=>{const e=(0,i.ConfigurationSchema)("LinearPairedArcDisplay",{color:{type:"color",description:"the color of the arcs",defaultValue:"jexl:defaultPairedArcColor(feature,alt)",contextVariable:["feature","alt"]}},{baseConfiguration:Rt.Ki,explicitlyTyped:!0});return new Q.DisplayType({name:"LinearPairedArcDisplay",displayName:"Arc display",configSchema:e,stateModel:ir(e),trackType:"VariantTrack",viewType:"LinearGenomeView",ReactComponent:(0,w.lazy)((()=>r.e(7126).then(r.bind(r,87126))))})}))}(e),e.jexl.addFunction("logThickness",((e,t)=>Math.log(e.get(t)+1))),e.jexl.addFunction("defaultPairedArcColor",((e,t)=>t?.startsWith("<DEL")?br.set1[0]:t?.startsWith("<DUP")?br.set1[1]:t?.startsWith("<INV")?br.set1[2]:t?.startsWith("<TRA")?br.set1[3]:t?.startsWith("<CNV")?br.set1[4]:br.set1[6]))}}var vr=r(67736),Cr=r(25914),Sr=r(36993);const kr=(0,i.ConfigurationSchema)("AboutWidget",{}),Tr=d.types.model("AboutWidget",{id:K.ElementId,type:d.types.literal("AboutWidget")}),xr=(0,i.ConfigurationSchema)("HelpWidget",{}),Ar=d.types.model("HelpWidget",{id:K.ElementId,type:d.types.literal("HelpWidget")}),Pr=(0,i.ConfigurationSchema)("ImportSessionWidget",{}),Mr=d.types.model("ImportSessionWidget",{id:K.ElementId,type:d.types.literal("ImportSessionWidget")}),Er=(0,i.ConfigurationSchema)("SessionManager",{}),Rr=d.types.model("SessionManager",{id:K.ElementId,type:d.types.literal("SessionManager")});class Ir extends a.A{name="MenusPlugin";install(e){e.addWidgetType((()=>new vr.A({name:"AboutWidget",heading:"About",configSchema:kr,stateModel:Tr,ReactComponent:(0,w.lazy)((()=>r.e(9032).then(r.bind(r,99032))))}))),e.addWidgetType((()=>new vr.A({name:"HelpWidget",heading:"Help",configSchema:xr,stateModel:Ar,ReactComponent:(0,w.lazy)((()=>r.e(4974).then(r.bind(r,74974))))}))),e.addWidgetType((()=>new vr.A({name:"ImportSessionWidget",heading:"Import session",configSchema:Pr,stateModel:Mr,ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(3778),r.e(7389)]).then(r.bind(r,67389))))}))),e.addWidgetType((()=>new vr.A({name:"SessionManager",heading:"Sessions",configSchema:Er,stateModel:Rr,ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(3162),r.e(8762)]).then(r.bind(r,58762))))})))}configure(e){(0,c.isAbstractMenuManager)(e.rootModel)&&(e.rootModel.appendToMenu("Help",{label:"About",icon:Sr.A,onClick:e=>{const t=e.addWidget("AboutWidget","aboutWidget");e.showWidget(t)}}),e.rootModel.appendToMenu("Help",{label:"Help",icon:Cr.A,onClick:e=>{const t=e.addWidget("HelpWidget","helpWidget");e.showWidget(t)}}))}}var Nr=r(46377),Fr=r(66885),Lr=r(6434),Dr=r(2401),Br=r.n(Dr);class Vr extends Nr.BaseFeatureDataAdapter{constructor(e,t,r){super(e,t,r),this.endpoint=(0,i.readConfObject)(e,"endpoint").uri,this.queryTemplate=(0,i.readConfObject)(e,"queryTemplate"),this.additionalQueryParams=(0,i.readConfObject)(e,"additionalQueryParams"),this.refNamesQueryTemplate=(0,i.readConfObject)(e,"refNamesQueryTemplate"),this.configRefNames=(0,i.readConfObject)(e,"refNames")}async getRefNames(e={}){if(this.refNames)return this.refNames;if(this.refNamesQueryTemplate){const t=encodeURIComponent(this.refNamesQueryTemplate),r=await this.querySparql(t,e);this.refNames=this.resultsToRefNames(r)}else this.refNames=this.configRefNames;return this.refNames}getFeatures(e,t={}){return(0,Fr.ObservableCreate)((async r=>{const n=encodeURIComponent(Br()(this.queryTemplate,e)),{refName:a}=e,o=await this.querySparql(n,t);this.resultsToFeatures(o,a).forEach((e=>{r.next(e)})),r.complete()}),t.signal)}async querySparql(e,t){let r="";this.additionalQueryParams.length&&(r=`&${this.additionalQueryParams.join("&")}`);const n=t?.signal;return(await fetch(`${this.endpoint}?query=${e}${r}`,{headers:{accept:"application/json,application/sparql-results+json"},signal:n})).json()}resultsToRefNames(e){const t=e.results.bindings||[];if(!e.head.vars.includes("refName"))throw new Error('"refName" not found in refNamesQueryTemplate response');return t.map((e=>e.refName.value))}resultsToFeatures(e,t){const r=e.results.bindings||[],n=e.head.vars;["start","end","uniqueId"].forEach((e=>{n.includes(e)||console.error(`Required field ${e} missing from feature data`)}));const a={};r.forEach((e=>{const r=[{}];n.forEach((t=>{if(t in e){const{value:n}=e[t];let a=0;for(;t.startsWith("sub_");)t=t.slice(4),a+=1;for(;a>r.length-1;)r.push({});r[a][t]=n}})),r.forEach(((e,n)=>{const{uniqueId:o,start:i,end:s,strand:l}=e;n<r.length-1&&(r[n+1].parentUniqueId=o),a[o]={data:{...e,uniqueId:o,refName:t,start:Number.parseInt(i,10),end:Number.parseInt(s,10),strand:Number.parseInt(l,10)||0}}}))}));for(const[e,t]of Object.entries(a)){const r=t.data.parentUniqueId;if(t.data.parentUniqueId=void 0,r){const n=a[r];if(n)n.data.subfeatures||(n.data.subfeatures=[]),n.data.subfeatures.push({...t.data,uniqueId:e}),delete a[e];else{const n=Object.values(a).map((e=>e.data.subfeatures)).filter((e=>!!e)).flat();let o=!1;for(const i of n){if(i.uniqueId===r){i.subfeatures||(i.subfeatures=[]),i.subfeatures.push({...t.data,uniqueId:e}),delete a[e],o=!0;break}i.subfeatures&&n.push(...i.subfeatures)}o||console.error(`Could not find parentID ${r}`)}}}return Object.keys(a).map((e=>new Lr.A({...a[e].data,uniqueId:e,subfeatures:a[e].data.subfeatures})))}async hasDataForRefName(e,t={}){const r=await this.getRefNames(t);return!(r.length&&!r.includes(e))}freeResources(){}}const zr=(0,i.ConfigurationSchema)("SPARQLAdapter",{endpoint:{type:"fileLocation",defaultValue:{uri:"https://somesite.com/sparql",locationType:"UriLocation"},description:"URL of the SPARQL endpoint"},queryTemplate:{type:"text",defaultValue:"",description:"SPARQL query where {start} {end} and {refName} will get replaced for each call"},refNamesQueryTemplate:{type:"text",defaultValue:"",description:"SPARQL query that returns the possible refNames in a ?refName column"},refNames:{type:"stringArray",defaultValue:[],description:'Possible refNames used by the SPARQL endpoint (ignored if "refNamesQueryTemplate" is provided)'},additionalQueryParams:{type:"stringArray",defaultValue:[],description:'Additional parameters to add to the query, e.g. "format=JSON"'}},{explicitlyTyped:!0});class Or extends a.A{name="RdfPlugin";install(e){e.addAdapterType((()=>new $.A({name:"SPARQLAdapter",displayName:"SPARQL adapter",configSchema:zr,AdapterClass:Vr}))),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="SPARQLAdapter",o=(0,X.getFileName)(t);return/\/sparql$/i.test(o)||n===a?{type:a,endpoint:t}:e(t,r,n)}))}}const Hr=(0,i.ConfigurationSchema)("TwoBitAdapter",{twoBitLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.2bit",locationType:"UriLocation"}},chromSizesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/default.chrom.sizes",locationType:"UriLocation"},description:"An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time"}},{explicitlyTyped:!0});function jr(){return jr=Object.assign?Object.assign.bind():function(e){for(var t=1;t<arguments.length;t++){var r=arguments[t];for(var n in r)({}).hasOwnProperty.call(r,n)&&(e[n]=r[n])}return e},jr.apply(null,arguments)}function Wr({codonTable:e,seq:t,frame:r,bpPerPx:n,colorByCDS:a,region:o,seqStart:i,height:s,y:l,reverse:d=!1,theme:u}){const p=(Math.abs(r)-1-i%3+3)%3,m=t.length-p,g=m-m%3,h=t.slice(p,p+g),f=[];for(let t=0;t<h.length;t+=3){const r=h.slice(t,t+3),n=d?(0,c.revcom)(r):r,a=e[n]||"";f.push({letter:a,codon:n.toUpperCase()})}const y=(o.end-o.start)/n,b=1/n*3,v=1/n>=12,C=p/n-(o.start-i)/n,S=a?u?.palette.framesCDS.at(r)?.main:u?.palette.frames.at(r)?.main;return w.createElement(w.Fragment,null,w.createElement("rect",{x:0,y:l,width:y,height:s,fill:S}),f.map(((e,t)=>{const r=o.reversed?y-(t+1)*b-C:b*t+C,{letter:n,codon:a}=e,i=c.defaultStarts.includes(a)?u?.palette.startCodon:c.defaultStops.includes(a)?u?.palette.stopCodon:void 0;return v||i?w.createElement(w.Fragment,{key:`${t}-${n}`},w.createElement("rect",{x:r,y:l,width:v?b:b+.7,height:s,stroke:v?"#555":"none",fill:i||"none"}),v?w.createElement("text",{x:r+b/2,fontSize:s-2,y:l+s/2,dominantBaseline:"middle",textAnchor:"middle"},n):null):null})))}function Gr({bpPerPx:e,region:t,feature:r,sequenceType:n,theme:a,height:o,seq:i,y:s}){const l=1/e>=12,d=r.get("start"),u=r.get("end"),[p,m]=(0,c.bpSpanPx)(d,u,t,e),g=t.reversed,h=u-d,f=Math.max((m-p)/h,.8);return w.createElement(w.Fragment,null,i.split("").map(((e,t)=>{const r="dna"===n?a.palette.bases[e.toUpperCase()]:void 0,i=g?m-(t+1)*f:p+t*f;return w.createElement(w.Fragment,{key:`${e}-${t}`},w.createElement("rect",{x:i,y:s,width:f,height:o,fill:r?r.main:"#aaa",stroke:l?"#555":"none"}),l?w.createElement("text",{x:i+f/2,y:s+o/2,dominantBaseline:"middle",textAnchor:"middle",fontSize:o-2,fill:r?a.palette.getContrastText(r.main):"black"},e):null)})))}function $r({regions:e,theme:t,colorByCDS:r,features:n=new Map,showReverse:a=!0,showForward:o=!0,showTranslation:i=!0,sequenceType:s="dna",bpPerPx:l,rowHeight:d}){const u=e[0],p=(0,T.createJBrowseTheme)(t),m=(0,c.generateCodonTable)(c.defaultCodonTable),[g]=[...n.values()];if(!g)return null;const h=g.get("seq");if(!h)return null;let f=-d;const y=l<=1,b=i&&o?[3,2,1]:[],v=i&&a?[-1,-2,-3]:[],[C,S]=u.reversed?[v.toReversed(),b.toReversed()]:[b,v];return w.createElement(w.Fragment,null,C.map((e=>w.createElement(Wr,{key:`translation-${e}`,colorByCDS:r,seq:h,y:f+=d,codonTable:m,frame:e,bpPerPx:l,region:u,seqStart:g.get("start"),theme:p,height:d,reverse:u.reversed}))),o&&y?w.createElement(Gr,{height:d,sequenceType:s,y:f+=d,feature:g,region:u,seq:u.reversed?(0,c.complement)(h):h,bpPerPx:l,theme:p}):null,a&&y?w.createElement(Gr,{height:d,sequenceType:s,y:f+=d,feature:g,region:u,seq:u.reversed?h:(0,c.complement)(h),bpPerPx:l,theme:p}):null,S.map((e=>w.createElement(Wr,{key:`rev-translation-${e}`,colorByCDS:r,seq:h,y:f+=d,codonTable:m,frame:e,bpPerPx:l,region:u,seqStart:g.get("start"),theme:p,height:d,reverse:!u.reversed}))))}function qr({exportSVG:e,width:t,totalHeight:r,children:n}){return e?n:w.createElement("svg",{"data-testid":"sequence_track",width:t,height:r,style:{display:"block",width:t,height:r,userSelect:"none"}},n)}const _r=(0,We.observer)((function(e){const{regions:t,bpPerPx:r,sequenceHeight:n}=e,a=t[0],o=(a.end-a.start)/r;return w.createElement(qr,jr({},e,{totalHeight:n,width:o}),w.createElement($r,e))})),Ur=(0,i.ConfigurationSchema)("DivSequenceRenderer",{height:{type:"number",description:"height in pixels of each line of sequence",defaultValue:16}},{explicitlyTyped:!0});class Jr extends fr.default{supportsSVG=!0;getExpandedRegion(e){return{...e,start:Math.max(e.start-3,0),end:e.end+3}}}const Xr=(0,i.ConfigurationSchema)("BgzipFastaAdapter",{fastaLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa.gz",locationType:"UriLocation"}},faiLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa.gz.fai",locationType:"UriLocation"}},metadataLocation:{description:"Optional metadata file",type:"fileLocation",defaultValue:{uri:"/path/to/fa.metadata.yaml",locationType:"UriLocation"}},gziLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa.gz.gzi",locationType:"UriLocation"}}},{explicitlyTyped:!0}),Yr=(0,i.ConfigurationSchema)("ChromSizesAdapter",{chromSizesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/species.chrom.sizes",locationType:"UriLocation"}}},{explicitlyTyped:!0}),Kr=(0,i.ConfigurationSchema)("IndexedFastaAdapter",{fastaLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa",locationType:"UriLocation"}},faiLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa.fai",locationType:"UriLocation"}},metadataLocation:{description:"Optional metadata file",type:"fileLocation",defaultValue:{uri:"/path/to/fa.metadata.yaml",locationType:"UriLocation"}}},{explicitlyTyped:!0}),Qr=(0,i.ConfigurationSchema)("UnindexedFastaAdapter",{rewriteRefNames:{type:"string",defaultValue:"",contextVariable:["refName"]},fastaLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/seq.fa",locationType:"UriLocation"}},metadataLocation:{description:"Optional metadata file",type:"fileLocation",defaultValue:{uri:"/path/to/fa.metadata.yaml",locationType:"UriLocation"}}},{explicitlyTyped:!0}),Zr=(0,i.ConfigurationSchema)("SequenceSearchAdapter",{search:{type:"string",defaultValue:"",description:"Search string or regex to search for"},sequenceAdapter:{type:"frozen",defaultValue:null},searchForward:{type:"boolean",defaultValue:!0},searchReverse:{type:"boolean",defaultValue:!0},caseInsensitive:{type:"boolean",defaultValue:!0}},{explicitlyTyped:!0});const en=(0,i.ConfigurationSchema)("LinearReferenceSequenceDisplay",{renderer:Ur},{explicitIdentifier:"displayId",explicitlyTyped:!0});class tn extends a.A{name="SequencePlugin";install(e){!function(e){e.addRendererType((()=>new Jr({name:"DivSequenceRenderer",ReactComponent:_r,configSchema:Ur,pluginManager:e})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"TwoBitAdapter",displayName:"TwoBit adapter",configSchema:Hr,adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>r.e(9280).then(r.bind(r,79280)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"BgzipFastaAdapter",displayName:"Bgzip-indexed FASTA adapter",configSchema:Xr,adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>Promise.all([r.e(7864),r.e(9086),r.e(2977),r.e(9206)]).then(r.bind(r,79206)).then((e=>e.default))})))}(e),function(e){e.addAdapterType((()=>new $.A({name:"ChromSizesAdapter",displayName:"Chrom sizes 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t=function(e){return(0,i.ConfigurationSchema)("ReferenceSequenceTrack",{adapter:e.pluggableConfigSchemaType("adapter"),displays:d.types.array(e.pluggableConfigSchemaType("display")),name:{type:"string",description:'optional track name, otherwise uses the "Reference sequence (assemblyName)"',defaultValue:""},sequenceType:{type:"string",description:"either dna or pep",defaultValue:"dna"},description:{description:"a description of the track",type:"string",defaultValue:""},metadata:{type:"frozen",description:"anything to add about this track",defaultValue:{}},formatAbout:(0,i.ConfigurationSchema)("FormatAbout",{config:{type:"frozen",description:"formats configuration in about dialog",defaultValue:{},contextVariable:["config"]},hideUris:{type:"boolean",defaultValue:!1}})},{preProcessSnapshot:t=>{const r=JSON.parse(JSON.stringify(t)),n=new Set,{displays:a=[]}=r;if("placeholderId"!==r.trackId){a.forEach((e=>e&&n.add(e.type)));const t=e.getTrackType(r.type);t?.displayTypes.forEach((e=>{n.has(e.name)||a.push({displayId:`${r.trackId}-${e.name}`,type:e.name})}))}return{...r,displays:a}},explicitIdentifier:"trackId",explicitlyTyped:!0,actions:e=>({addDisplayConf(t){const{type:r}=t;if(!r)throw new Error(`unknown display type ${r}`);const n=e.displays.find((e=>e&&e.displayId===t.displayId));if(n)return n;const a=e.displays.push(t);return e.displays[a-1]}})})}(e);return new _t.A({name:"ReferenceSequenceTrack",displayName:"Reference sequence track",configSchema:t,stateModel:(0,s.createBaseTrackModel)(e,"ReferenceSequenceTrack",t)})}))}(e),function(e){e.addDisplayType((()=>{const e=function(e){return d.types.compose("LinearReferenceSequenceDisplay",Rt.Lr,d.types.model({type:d.types.literal("LinearReferenceSequenceDisplay"),configuration:(0,i.ConfigurationReference)(e),showForward:!0,showReverse:!0,showTranslation:!0})).volatile((()=>({rowHeight:15}))).views((e=>({get sequenceType(){return(0,i.getConf)((0,c.getContainingTrack)(e),"sequenceType")},get showForwardActual(){return e.showForward},get showReverseActual(){return"dna"===this.sequenceType&&e.showReverse},get showTranslationActual(){return"dna"===this.sequenceType&&e.showTranslation}}))).views((e=>({get sequenceHeight(){const{rowHeight:t,showTranslationActual:r,showReverseActual:n,showForwardActual:a}=e;return(n&&r?3*t:0)+(a&&r?3*t:0)+(n?t:0)+(a?t:0)}}))).views((e=>{const{renderProps:t}=e;return{renderProps(){const{rpcDriverName:r,showForwardActual:n,showReverseActual:a,showTranslationActual:o,rowHeight:i,sequenceHeight:s,sequenceType:l}=e;return{...t(),...(0,X.getParentRenderProps)(e),config:e.configuration.renderer,rpcDriverName:r,showForward:n,showReverse:a,showTranslation:o,sequenceType:l,rowHeight:i,sequenceHeight:s}}}})).views((e=>({regionCannotBeRendered:()=>(0,c.getContainingView)(e).bpPerPx>3?"Zoom in to see sequence":void 0,get rendererTypeName(){return e.configuration.renderer.type}}))).actions((e=>({toggleShowForward(){e.showForward=!e.showForward},toggleShowReverse(){e.showReverse=!e.showReverse},toggleShowTranslation(){e.showTranslation=!e.showTranslation},afterAttach(){(0,d.addDisposer)(e,(0,ae.autorun)((()=>{(0,c.getContainingView)(e).bpPerPx>3?e.setHeight(50):e.setHeight(e.sequenceHeight)})))}}))).views((e=>({trackMenuItems:()=>[..."dna"===e.sequenceType?[{label:"Show forward",type:"checkbox",checked:e.showForward,onClick:()=>{e.toggleShowForward()}},{label:"Show reverse",type:"checkbox",checked:e.showReverse,onClick:()=>{e.toggleShowReverse()}},{label:"Show translation",type:"checkbox",checked:e.showTranslation,onClick:()=>{e.toggleShowTranslation()}}]:[]]})))}(en);return new Q.DisplayType({name:"LinearReferenceSequenceDisplay",configSchema:en,stateModel:e,displayName:"Reference sequence 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e.forEach(((e,n)=>{if(t.includes(n))return;let{text:a}=r.cells[n];"Number"===e.dataType.type&&(a=Number.parseFloat(a)),i[e.name]=a})),{...i,uniqueId:`sv-inspector-adhoc-${o}`,refName:n.refName,start:n.start,end:n.end,mate:{refName:a.refName,start:a.start,end:a.end}}}function qa(e,t,r,n){return r.extendedData?.vcfFeature||r.extendedData?.feature||function(e,t,r,n){const{columns:a,columnDisplayOrder:o}=e,i={};o.forEach((e=>{const t=a[e];i[t.dataType.type]||(i[t.dataType.type]=[]),i[t.dataType.type].push(e)}));const s=i.LocString||[],l=i.LocStart||[],d=i.LocEnd||[],u=i.LocRef||[];return s.length>=2?function(e,t,r,n,a){const o=(0,c.parseLocString)(r.cells[t[0]].text,a),i=(0,c.parseLocString)(r.cells[t[1]].text,a);return $a(e,[t[0],t[1]],r,o,i,n)}(a,s,r,t,n):u.length>=2&&l.length>=2&&d.length>=2?function(e,t,r,n,a,o){const i=e=>a.cells[e].text,s={refName:i(t[0]),start:Number.parseInt(i(r[0]),10)-1,end:Number.parseInt(i(n[0]),10)},l={refName:i(t[1]),start:Number.parseInt(i(r[1]),10)-1,end:Number.parseInt(i(n[1]),10)};return $a(e,[t[0],r[0],n[0],t[1],r[1],n[1]],a,s,l,o)}(a,u,l,d,r,t):void 0}(t.spreadsheet,n,r,e.assemblyManager.isValidRefName)}function _a(e,t,r,n,a){const{pluginManager:o}=(0,c.getEnv)(e),i=(0,c.getSession)(t),s=qa(i,r,n,a);if(s){const t=new c.SimpleFeature(s);return i.setSelection(t),o.getViewType("BreakpointSplitView").snapshotFromBreakendFeature(t,e.circularView)}}function Ua(e,t,r){const n=(0,c.getSession)(t);n.setSelection(e);const a=(0,c.getContainingView)(t),o=r.getViewType("BreakpointSplitView").snapshotFromBreakendFeature(e,a);o.views[0].offsetPx-=a.width/2+100,o.views[1].offsetPx-=a.width/2+100,n.addView("BreakpointSplitView",o)}class Ja extends a.A{name="SvInspectorViewPlugin";install(e){!function(e){e.jexl.addFunction("defaultOnChordClick",Ua),e.addViewType((()=>{const t=function(e){const t=e.getViewType("SpreadsheetView"),r=e.getViewType("CircularView"),n=t.stateModel,a=r.stateModel;return d.types.compose("SvInspectorView",s.BaseViewModel,d.types.model({id:K.ElementId,type:d.types.literal("SvInspectorView"),height:d.types.optional(d.types.refinement("SvInspectorViewHeight",d.types.number,(e=>e>=400)),550),onlyDisplayRelevantRegionsInCircularView:!1,mode:d.types.optional(d.types.enumeration("SvInspectorViewMode",["import","display"]),"import"),spreadsheetView:d.types.optional(n,(()=>n.create({type:"SpreadsheetView",hideVerticalResizeHandle:!0}))),circularView:d.types.optional(a,(()=>a.create({type:"CircularView",hideVerticalResizeHandle:!0,hideTrackSelectorButton:!0,disableImportForm:!0})))})).volatile((()=>({width:800}))).views((e=>({get selectedRows(){return e.spreadsheetView.spreadsheet?.rowSet.selectedRows},get assemblyName(){const{assembly:t}=e.spreadsheetView;return t?(0,i.readConfObject)(t,"name"):void 0},get showCircularView(){return"display"===e.spreadsheetView.mode},get features(){const t=(0,c.getSession)(e),{spreadsheetView:r}=e,{outputRows:n=[]}=r;return n.map(((e,n)=>qa(t,r,e,n))).filter((e=>!!e))},get featuresAdapterConfigSnapshot(){return{type:"FromConfigAdapter",features:this.features}},get featureRefNames(){return[...this.features.map((e=>e.refName)),...this.features.flatMap((e=>e.INFO?.CHR2)).filter((e=>!!e))]},get featuresCircularTrackConfiguration(){return{type:"VariantTrack",trackId:`sv-inspector-variant-track-${e.id}`,name:"features from tabular data",adapter:this.featuresAdapterConfigSnapshot,assemblyNames:[this.assemblyName],displays:[{type:"ChordVariantDisplay",displayId:`sv-inspector-variant-track-chord-display-${e.id}`,onChordClick:"jexl:defaultOnChordClick(feature, track, pluginManager)",renderer:{type:"StructuralVariantChordRenderer"}}]}}}))).volatile((()=>({SpreadsheetViewReactComponent:t.ReactComponent,CircularViewReactComponent:r.ReactComponent,circularViewOptionsBarHeight:52}))).actions((e=>({setWidth(t){e.width=t},setHeight:t=>(e.height=t>400?t:400,e.height),setImportMode(){e.spreadsheetView.setImportMode()},setDisplayMode(){e.spreadsheetView.setDisplayMode()},setDisplayedRegions(t){e.circularView.setDisplayedRegions(t)},setOnlyDisplayRelevantRegionsInCircularView(t){e.onlyDisplayRelevantRegionsInCircularView=Boolean(t)}}))).views((e=>({menuItems:()=>[{label:"Return to import form",onClick:()=>{e.setImportMode()},icon:Me.A}]}))).actions((e=>({resizeHeight(t){const r=e.height;return e.setHeight(e.height+t)-r},afterAttach(){(0,d.addDisposer)(e,(0,ae.autorun)((()=>{if(e.showCircularView){const t=Math.round(.66*e.width),r=e.width-t;e.spreadsheetView.setWidth(t-1),e.circularView.setWidth(r)}else e.spreadsheetView.setWidth(e.width)}),{name:"SvInspectorView width binding"})),(0,d.addDisposer)(e,(0,ae.autorun)((()=>{e.spreadsheetView.setHeight(e.height-52),e.circularView.setHeight(e.height-52-52)}),{name:"SvInspectorView height binding"})),(0,d.addDisposer)(e,(0,ae.autorun)((async()=>{const{assemblyName:t,onlyDisplayRelevantRegionsInCircularView:r,circularView:n,featureRefNames:a}=e,{tracks:o}=n,{assemblyManager:i}=(0,c.getSession)(e);if(!t)return;const s=await i.waitForAssembly(t);if(!s)return;const{getCanonicalRefName:l,regions:d=[]}=s;if(r){if(1===o.length)try{const e=new Set(a.map((e=>l(e)||e)));n.setDisplayedRegions(Ye()(d.filter((t=>e.has(t.refName)))))}catch(e){n.setError(e)}}else n.setDisplayedRegions(d)}),{name:"SvInspectorView displayed regions 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Ka=(0,We.observer)((function(e){const{width:t,height:r}=e,n=Math.ceil(t);return w.createElement("div",{style:{position:"relative",width:n,height:r}},w.createElement(T.PrerenderedCanvas,Ya({},e,{style:{position:"absolute",left:0,top:0}})))})),Qa=(0,i.ConfigurationSchema)("HicRenderer",{baseColor:{type:"color",description:"base color to be used in the hic alignment",defaultValue:"#f00"},color:{type:"color",description:"the color of each feature in a hic alignment",defaultValue:"jexl:interpolate(count,scale)",contextVariable:["count","maxScore","baseColor","scale"]},maxHeight:{type:"integer",description:"the maximum height to be used in a hic rendering",defaultValue:600}},{explicitlyTyped:!0});var Za=r(198),eo=r(98506),to=r(82088),ro=r(3496),no=r(44728);class ao extends Za.default{supportsSVG=!0;async render(e){const{config:t,regions:n,bpPerPx:a}=e,o=n[0],s=(o.end-o.start)/a,l=(0,i.readConfObject)(t,"maxHeight"),c=await this.getFeatures(e),{makeImageData:d}=await r.e(9088).then(r.bind(r,49088)),u=await(0,eo.u1)(s,l,e,(t=>d(t,{...e,features:c,pluginManager:this.pluginManager})));return{...await super.render({...e,...u,features:c,region:e.regions[0],height:l,width:s}),...u,height:l,width:s}}async getFeatures(e){const{regions:t,sessionId:r,adapterConfig:n}=e,{dataAdapter:a}=await(0,ro.cK)(this.pluginManager,r,n);return await(0,no._)(a.getFeatures(t[0],e).pipe((0,to.$)()))}}function oo(e){return d.types.compose("LinearHicDisplay",Rt.Lr,d.types.model({type:d.types.literal("LinearHicDisplay"),configuration:(0,i.ConfigurationReference)(e),resolution:d.types.optional(d.types.number,1),useLogScale:!1,colorScheme:d.types.maybe(d.types.string)})).views((e=>{const{renderProps:t}=e;return{get blockType(){return"dynamicBlocks"},get rendererTypeName(){return"HicRenderer"},renderProps(){const r=e.rendererType.configSchema.create({...(0,i.getConf)(e,"renderer"),...e.colorScheme?{color:"jexl:interpolate(count,scale)"}:{}},(0,d.getEnv)(e));return{...t(),config:r,rpcDriverName:e.rpcDriverName,displayModel:e,resolution:e.resolution,useLogScale:e.useLogScale,colorScheme:e.colorScheme}}}})).actions((e=>({setResolution(t){e.resolution=t},setUseLogScale(t){e.useLogScale=t},setColorScheme(t){e.colorScheme=t}}))).views((e=>{const{trackMenuItems:t}=e;return{trackMenuItems:()=>[...t(),{label:"Use log scale",type:"checkbox",checked:e.useLogScale,onClick:()=>{e.setUseLogScale(!e.useLogScale)}},{label:"Color scheme",type:"subMenu",subMenu:[{label:"Fall",onClick:()=>{e.setColorScheme("fall")}},{label:"Viridis",onClick:()=>{e.setColorScheme("viridis")}},{label:"Juicebox",onClick:()=>{e.setColorScheme("juicebox")}},{label:"Clear",onClick:()=>{e.setColorScheme(void 0)}}]},{label:"Resolution",subMenu:[{label:"Finer resolution",onClick:()=>{e.setResolution(2*e.resolution)}},{label:"Coarser resolution",onClick:()=>{e.setResolution(e.resolution/2)}}]}]}}))}const io=(0,i.ConfigurationSchema)("HicAdapter",{hicLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.hic",locationType:"UriLocation"}}},{explicitlyTyped:!0});class so extends a.A{name="HicPlugin";install(e){!function(e){e.addAdapterType((()=>new Q.AdapterType({name:"HicAdapter",displayName:"Hi-C adapter",configSchema:io,getAdapterClass:()=>Promise.all([r.e(6514),r.e(937)]).then(r.bind(r,90937)).then((e=>e.default))})))}(e),function(e){e.addRendererType((()=>new ao({name:"HicRenderer",ReactComponent:Ka,configSchema:Qa,pluginManager:e})))}(e),function(e){e.addTrackType((()=>{const t=(e=>(0,i.ConfigurationSchema)("HicTrack",{},{baseConfiguration:(0,Q.createBaseTrackConfig)(e)}))(e);return new _t.A({name:"HicTrack",displayName:"Hi-C track",configSchema:t,stateModel:(0,s.createBaseTrackModel)(e,"HicTrack",t)})}))}(e),function(e){e.addDisplayType((()=>{const t=(e=>(0,i.ConfigurationSchema)("LinearHicDisplay",{renderer:e.getRendererType("HicRenderer").configSchema},{baseConfiguration:Rt.Ki,explicitlyTyped:!0}))(e);return new Q.DisplayType({name:"LinearHicDisplay",displayName:"Hi-C contact matrix display",configSchema:t,stateModel:oo(t),trackType:"HicTrack",viewType:"LinearGenomeView",ReactComponent:Rt.GQ})}))}(e),e.addToExtensionPoint("Core-guessAdapterForLocation",(e=>(t,r,n)=>{const a="HicAdapter",o=(0,X.getFileName)(t),i={type:a,hicLocation:t};return/\.hic/i.test(o)&&!n||n===a?i:e(t,r,n)})),e.addToExtensionPoint("Core-guessTrackTypeForLocation",(e=>t=>"HicAdapter"===t?"HicTrack":e(t)))}configure(e){const{jexl:t}=e;t.addFunction("alpha",((e,t)=>e.alpha(t))),t.addFunction("hsl",(e=>(0,Xa.M)(e.toHsl()))),t.addFunction("colorString",(e=>e.toHex())),t.addFunction("interpolate",((e,t)=>t(e)))}}const lo=(0,i.ConfigurationSchema)("TrixTextSearchAdapter",{ixFilePath:{type:"fileLocation",defaultValue:{uri:"out.ix",locationType:"UriLocation"},description:"the location of the trix ix file"},ixxFilePath:{type:"fileLocation",defaultValue:{uri:"out.ixx",locationType:"UriLocation"},description:"the location of the trix ixx file"},metaFilePath:{type:"fileLocation",defaultValue:{uri:"meta.json",locationType:"UriLocation"},description:"the location of the metadata json file for the trix index"},tracks:{type:"stringArray",defaultValue:[],description:"List of tracks covered by text search adapter"},assemblyNames:{type:"stringArray",defaultValue:[],description:"List of assemblies covered by text search adapter"}},{explicitlyTyped:!0,explicitIdentifier:"textSearchAdapterId"});class co extends a.A{name="TrixPlugin";install(e){e.addTextSearchAdapterType((()=>new Tt.A({name:"TrixTextSearchAdapter",displayName:"Trix text search adapter",configSchema:lo,description:"Trix text search adapter",getAdapterClass:()=>r.e(5260).then(r.bind(r,15260)).then((e=>e.default))})))}}var uo=r(11353),po=r(29948),mo=r(17037),go=r(95947);const ho=d.types.compose(K.Region,d.types.model("Label",{label:d.types.optional(d.types.string,""),highlight:d.types.optional(d.types.string,"rgba(247, 129, 192, 0.35)")})).actions((e=>({setLabel(t){e.label=t},setHighlight(t){e.highlight=t}}))),fo=d.types.model("SharedBookmarksModel",{sharedBookmarks:d.types.maybe(d.types.array(ho))}),yo=()=>"undefined"!=typeof window?`bookmarks-${[window.location.host+window.location.pathname].join("-")}`:"empty";var bo=r(89003),wo=r(23758);const vo=(0,He.n9)()({highlight:{overflow:"hidden",height:"100%",position:"absolute",zIndex:100,pointerEvents:"none"},highlightButton:{pointerEvents:"auto"}}),Co=(0,We.observer)((function({model:e}){const{classes:t}=vo(),r=(0,c.getSession)(e),{assemblyManager:n}=r,{showBookmarkHighlights:a,showBookmarkLabels:o}=e,i=r.widgets.get("GridBookmark");(0,w.useEffect)((()=>{i||r.addWidget("GridBookmarkWidget","GridBookmark")}),[r,i]);const s=new Set(e.assemblyNames);return a&&i?.bookmarks?i.bookmarks.filter((e=>s.has(e.assemblyName))).map((t=>{const r=n.get(t.assemblyName),a=r?.getCanonicalRefName(t.refName)??t.refName,o=e.bpToPx({refName:a,coord:t.start}),i=e.bpToPx({refName:a,coord:t.end});return o&&i?{width:Math.max(Math.abs(i.offsetPx-o.offsetPx),3),left:Math.min(o.offsetPx,i.offsetPx)-e.offsetPx,highlight:t.highlight,label:t.label,bookmark:t}:void 0})).filter(c.notEmpty).map((({left:e,width:n,highlight:a,label:s,bookmark:l},c)=>w.createElement("div",{key:`${e}_${n}_${c}`,className:t.highlight,style:{left:e,width:n,background:a}},o?w.createElement("div",{className:t.highlightButton},w.createElement(wo.A,{menuItems:[{label:"Open bookmark widget",onClick:()=>{r.showWidget(i)}},{label:"Remove bookmark",onClick:()=>{i.removeBookmarkObject(l)}}]},w.createElement(bo.A,{title:s,arrow:!0},w.createElement(uo.A,{fontSize:"small",sx:{color:0!==(0,Xa.M)(a).alpha()?(0,Xa.M)(a).alpha(.8).toRgbString():(0,Xa.M)(a).alpha(0).toRgbString()}})))):null))):null})),So=Co,ko=(0,He.n9)()({highlight:{height:"100%",position:"absolute"}}),To=(0,We.observer)((function({model:e,overview:t}){const{cytobandOffset:r}=e,n=(0,c.getSession)(e),{classes:a}=ko(),{assemblyManager:o}=n,{showBookmarkHighlights:i,showBookmarkLabels:s}=e,l=n.widgets.get("GridBookmark");(0,w.useEffect)((()=>{l||n.addWidget("GridBookmarkWidget","GridBookmark")}),[n,l]);const d=new Set(e.assemblyNames);return i&&l?.bookmarks?l.bookmarks.filter((e=>d.has(e.assemblyName))).map((e=>{const n=o.get(e.assemblyName),a=n?.getCanonicalRefName(e.refName)??e.refName,i=e.reversed,s=t.bpToPx({refName:a,coord:i?e.end:e.start}),l=t.bpToPx({refName:a,coord:i?e.start:e.end});return void 0!==s&&void 0!==l?{width:Math.abs(l-s),left:s+r,highlight:e.highlight,label:e.label}:void 0})).filter(c.notEmpty).map(((e,t)=>{const{left:r,width:n,highlight:o,label:i}=e;return w.createElement(bo.A,{key:`${JSON.stringify(e)}-${t}`,title:s?i:"",arrow:!0},w.createElement("div",{className:a.highlight,style:{left:r,width:n,background:o,borderLeft:`1px solid ${o}`,borderRight:`1px solid ${o}`}}))})):null})),xo=To,Ao=(0,i.ConfigurationSchema)("GridBookmarkWidget",{});class Po extends a.A{name="GridBookmarkPlugin";install(e){(function(e){e.addWidgetType((()=>new Q.WidgetType({name:"GridBookmarkWidget",heading:"Bookmarked regions",configSchema:Ao,stateModel:d.types.model("GridBookmarkModel",{id:K.ElementId,type:d.types.literal("GridBookmarkWidget"),bookmarks:d.types.optional(d.types.array(ho),(()=>JSON.parse((0,c.localStorageGetItem)(yo())||"[]")))}).volatile((()=>({selectedBookmarks:[],selectedAssembliesPre:void 0}))).views((e=>({get bookmarkAssemblies(){return[...new Set(e.bookmarks.map((e=>e.assemblyName)))]},get validAssemblies(){const{assemblyManager:t}=(0,c.getSession)(e);return new Set(this.bookmarkAssemblies.filter((e=>t.get(e))))},get areBookmarksHighlightedOnAllOpenViews(){const{views:t}=(0,c.getSession)(e);return t.every((e=>!("showBookmarkHighlights"in e)||e.showBookmarkHighlights))},get areBookmarksHighlightLabelsOnAllOpenViews(){const{views:t}=(0,c.getSession)(e);return t.every((e=>!("showBookmarkLabels"in e)||e.showBookmarkLabels))}}))).views((e=>({get bookmarksWithValidAssemblies(){return e.bookmarks.filter((t=>e.validAssemblies.has(t.assemblyName)))}}))).views((e=>({get sharedBookmarksModel(){return fo.create({sharedBookmarks:JSON.parse(JSON.stringify(e.selectedBookmarks))})},get allBookmarksModel(){return fo.create({sharedBookmarks:JSON.parse(JSON.stringify(e.bookmarksWithValidAssemblies))})}}))).actions((e=>({setSelectedAssemblies(t){e.selectedAssembliesPre=t}}))).views((e=>({get selectedAssemblies(){return e.selectedAssembliesPre?.filter((t=>e.validAssemblies.has(t)))??[...e.validAssemblies]}}))).actions((e=>({importBookmarks(t){e.bookmarks=(0,d.cast)([...e.bookmarks,...t])},addBookmark(t){e.bookmarks.push(t)},removeBookmark(t){e.bookmarks.splice(t,1)},updateBookmarkLabel(e,t){e.correspondingObj.setLabel(t)},updateBookmarkHighlight(e,t){e.correspondingObj.setHighlight(t)},updateBulkBookmarkHighlights(t){e.selectedBookmarks.forEach((e=>{this.updateBookmarkHighlight(e,t)}))},setSelectedBookmarks(t){e.selectedBookmarks=t},setBookmarkedRegions(t){e.bookmarks=(0,d.cast)(t)},setHighlightToggle(t){const{views:r}=(0,c.getSession)(e);r.forEach((e=>{e.toggleShowBookmarkHighlights?.(t)}))},setLabelToggle(t){const{views:r}=(0,c.getSession)(e);r.forEach((e=>{e.toggleShowBookmarkLabels?.(t)}))}}))).actions((e=>({clearAllBookmarks(){e.setBookmarkedRegions(e.bookmarks.filter((t=>!e.validAssemblies.has(t.assemblyName))))},clearSelectedBookmarks(){for(const t of e.selectedBookmarks)e.bookmarks.remove(t.correspondingObj);e.selectedBookmarks=[]},removeBookmarkObject(t){e.bookmarks.remove(t)}}))).actions((e=>({afterAttach(){const t=yo();function r(r){if(r.key===t){const r=JSON.parse((0,c.localStorageGetItem)(t)||"[]");e.setBookmarkedRegions(r)}}window.addEventListener("storage",r),(0,d.addDisposer)(e,(()=>{window.removeEventListener("storage",r)})),(0,d.addDisposer)(e,(0,ae.autorun)((()=>{(0,c.localStorageSetItem)(t,JSON.stringify(e.bookmarks))})))}}))).postProcessSnapshot((e=>{const{bookmarks:t,...r}=e;return r})),ReactComponent:(0,w.lazy)((()=>Promise.all([r.e(8565),r.e(5676),r.e(5031),r.e(6395),r.e(3199)]).then(r.bind(r,53199))))}))),function(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",((e,{model:t})=>[...e||[],w.createElement(So,{key:"highlight_grid_bookmark",model:t})])),e.addToExtensionPoint("LinearGenomeView-OverviewScalebarComponent",((e,{model:t,overview:r})=>[...e||[],w.createElement(xo,{key:"overview_highlight_grid_bookmark",model:t,overview:r})]))}(e)})(e),e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearGenomeView"===e.name){const{stateModel:t}=e,r=t.props({showBookmarkHighlights:!0,showBookmarkLabels:!0}).actions((e=>({toggleShowBookmarkHighlights(t){e.showBookmarkHighlights=void 0!==t?t:!e.showBookmarkHighlights},toggleShowBookmarkLabels(t){e.showBookmarkLabels=void 0!==t?t:!e.showBookmarkLabels},activateBookmarkWidget(){const t=(0,c.getSession)(e);if((0,c.isSessionModelWithWidgets)(t)){let e=t.widgets.get("GridBookmark");return e||(e=t.addWidget("GridBookmarkWidget","GridBookmark")),t.showWidget(e),t.widgets.get("GridBookmark")}throw new Error("Could not open bookmark widget")}}))).actions((e=>({navigateNewestBookmark(){const t=(0,c.getSession)(e),r=e.activateBookmarkWidget();r.bookmarks.length?e.navTo(r.bookmarks.at(-1)):t.notify("There are no recent bookmarks to navigate to.","info")},bookmarkCurrentRegion(){if(e.id===(0,c.getSession)(e).focusedViewId){const t=e.getSelectedRegions(void 0,void 0),r=e.activateBookmarkWidget();if(!t.length)throw new Error("no region selected");r.addBookmark(t[0])}}}))).views((e=>{const t=e.menuItems,r=e.rubberBandMenuItems;return{menuItems:()=>[...t(),{type:"divider"},{label:"Bookmarks",icon:po.A,subMenu:[{label:"Open bookmark widget",icon:po.A,onClick:()=>e.activateBookmarkWidget()},{label:"Bookmark current region",icon:uo.A,onClick:()=>{e.bookmarkCurrentRegion()}},{label:"Toggle bookmark highlights",icon:mo.A,type:"checkbox",checked:e.showBookmarkHighlights,onClick:()=>{e.toggleShowBookmarkHighlights()}},{label:"Toggle bookmark labels",icon:go.A,type:"checkbox",checked:e.showBookmarkLabels,onClick:()=>{e.toggleShowBookmarkLabels()}}]}],rubberBandMenuItems:()=>[...r(),{label:"Bookmark region",icon:uo.A,onClick:()=>{const{leftOffset:t,rightOffset:r}=e,n=e.getSelectedRegions(t,r),a=e.activateBookmarkWidget();if(!n.length)throw new Error("no regions selected");a.addBookmark(n[0])}}]}})).actions((e=>({afterCreate(){document.addEventListener("keydown",(t=>{const r=(t.ctrlKey||t.metaKey)&&t.shiftKey;r&&"KeyD"===t.code&&(t.preventDefault(),e.activateBookmarkWidget(),e.bookmarkCurrentRegion(),(0,c.getSession)(e).notify("Bookmark created.","success")),r&&"KeyM"===t.code&&(t.preventDefault(),e.navigateNewestBookmark())}))}})));e.stateModel=r}return e}))}configure(e){(0,c.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToMenu("Tools",{label:"Bookmarks",icon:po.A,onClick:e=>{let t=e.widgets.get("GridBookmark");t||(t=e.addWidget("GridBookmarkWidget","GridBookmark")),e.showWidget(t)}})}}const Mo=[Ln,Rt.Ay,n.Ay,G,Y,ge.Ay,he.Ay,Te.A,gt,ft,wt,St,Et,Jt,ar,Ir,Or,tn,Dn.A,Bn.Ay,On,Na,Ja,me,so,co,Po,ke,wr]},52404:()=>{}}]);
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