jbrowse-plugin-graphgenomeviewer 4.0.20 → 4.0.21

package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

@@ -1,3 +1,3 @@
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e.colorScheme??e.defaultColorScheme}})).views(e=>({get paneWidth(){return(0,A.getContainingView)(e).width},get drawnGraph(){return e.layoutResult?.tubeMap?.coarse?.graph??e.graph}})).views(e=>({get nodeById(){if(e.drawnGraph){let t=new Map;for(let n of e.drawnGraph.nodes)t.set(n.id,n);return t}},get nodeLengths(){let t=new Map;for(let n of e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return Eo(e)},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!Eo(e))},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Pn(e.chosenLayoutMode,e.graph):!1},get canAnchorLayout(){return e.graph?.nodes.some(t=>t.stable?.rank===0)??!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&at(t.length)?it(t,n?.pathColors):[]},get walkChoices(){let t=e.graph?.paths;return t?.length?it(t):[]},get effectiveDrawPaths(){return e.drawPaths&&at(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){return e.colorDomain??e.graphRegion},get walkLift(){let{graph:t}=e;return t&&e.walkLayers.length>0?ro(t,e.walkLayers,st(t,this.rampDomain)):void 0},get effectiveColorScheme(){return fn(e.chosenColorScheme,e.graph)},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap},get rowLabels(){return e.layoutResult?.rowLabels??[]},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?vr(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get sourceAdapter(){let t=e.sourceTrack;return t?(0,te.readConfObject)(t,"adapter"):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,te.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,A.getSession)(e).tracks.filter(n=>(0,te.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,te.readConfObject)(n,"name"),adapterType:(0,te.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>xt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Tt.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return go(e.repeatTrackChoices,e.repeatTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?Qt(e.graph):void 0},assemblySpellings(t){let{assemblyManager:n}=(0,A.getSession)(e),r=n.has(t)?n.get(t):void 0,a=e.sourceAdapter?.assemblyNameToPanSN??{},o=[t,...r?[r.name,...r.aliases]:[]];return{name:t,aliases:[...o,...o.flatMap(i=>a[i]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0}})).views(e=>({get backboneGenes(){let{backbone:t,geneAssembly:n,geneFeatures:r}=e,a=e.drawsLoadedReference||n!==void 0&&en(t,[n])!==void 0;return t&&r&&a?nn(r,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?Ae(e.drawnGraph):void 0},get nodeInk(){return vn(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get deletions(){return 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t=e.layoutResult?.nodePositions;if(!e.showBubbles||e.chosenLayoutMode==="walkrows"||e.layoutResult?.tubeMap||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return Ir(e.graph,e.bubbles,t,r=>n.get(r)??r,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.graph&&!e.layoutResult?.tubeMap?st(e.graph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return Ve(e.scale,e.pixelRows).scaleX},get scaleY(){return Ve(e.scale,e.pixelRows).scaleY},get axisScale(){return Ve(e.scale,e.pixelRows)},get layoutBounds(){let t=e.layoutResult,n=this.walkRowBars;return t?zr(t,{region:e.popStack.length===0?e.graphRegion:void 0,extent:n&&t.extent?Gn(n):void 0}):void 0}})).views(e=>({get geneTrack(){return io(e.geneTrackChoices,e.geneTrackId)},get deletionEdgeIndexes(){return new Map(e.deletions.map(t=>[t.edgeIndex,t.bypassed]))},get hiddenEdgeIndexes(){return new 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r=e.layoutResult?.tubeMap,a=e.tubeMapFrame;return(r&&a?Zr(r,a,t,n):null)??jn(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}})).actions(e=>({setError(t){e.error=t,e.isLoading=!1,e.statusMessage=""},finishLoading(){e.isLoading=!1,e.statusMessage=""},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,n,r){e.lastGeometryMs=t,e.lastGeometryStrokeCount=n,e.builtViewport={...r,viewportDirty:e.viewportDirty},e.geometryVersion++},markPainted(){e.paintedViewport=e.builtViewport},setLayoutQuality(t){e.layoutQuality=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.layoutMode=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let 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0;(0,A.isSessionModelWithWidgets)(o)&&o.showWidget(o.addWidget("BaseFeatureWidget","baseFeature",{featureData:{id:n.id,name:n.name,length:n.length,depth:n.depth,rank:n.stable?.rank,stableName:n.stable?.refName,contributingAssembly:Ie(n)?.sample,contributingHaplotype:Ie(n)?.haplotype,carriedBy:n.samples?.join(", "),...i&&s?{refName:i.refName,assemblyName:i.assemblyName,start:s.start,end:s.end}:{}}}))}},setTransform(t,n,r){let{host:a}=e;e.viewportOwner==="host"&&a?a.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=he(t),e.translateX=n),e.translateY=r},zoom(t,n,r){let{host:a}=e;if(e.viewportOwner==="host"&&a){a.zoomTo(a.bpPerPx/t,n);return}e.viewportOwner="user";let o=to(e,t,n,r,e.pixelRows);e.scale=o.scale,e.translateX=o.translateX,e.translateY=o.translateY},setViewportDirty(){e.viewportRebuildPending=!1,e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){if(e.viewportOwner==="host"){let n=e.layoutBounds,r=e.canvasHeight-D*2;n&&r>0&&(e.translateY=wt(n,r,e.scaleY));return}let t=e.fittedTransform;t&&(e.scale=t.scale,e.translateX=t.translateX,e.translateY=t.translateY)},clearPerfMetrics(){e.lastFetchMs=void 0,e.lastLayoutMs=void 0,e.lastGeometryMs=void 0,e.lastGeometryStrokeCount=void 0,e.builtViewport=void 0}})).actions(e=>({hostTransform(t,n){let r=e.viewportOwner!=="host";r&&(e.viewportOwner="host"),e.scale=t,e.translateX=n,r&&e.zoomToFit()},releaseHost(){e.viewportOwner==="host"&&(e.xIsReferenceBp?e.viewportOwner="user":(e.viewportOwner="fit",e.zoomToFit()))}})).actions(e=>{function t(){clearTimeout(e.viewportDirtyTimer),e.viewportRebuildPending=!0,e.viewportDirtyTimer=setTimeout(()=>{(0,w.isAlive)(e)&&e.setViewportDirty()},ji)}function n(){cancelAnimationFrame(e.positionsDirtyFrame),e.positionsDirtyFrame=requestAnimationFrame(()=>{(0,w.isAlive)(e)&&e.setPositionsDirty()})}return{moveNode(r,a,o){let i=e.layoutResult?.nodePositions;if(i?.[r]){for(let s of 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n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,a=n&&r?He(r):void 0;a&&t.settleOn(a)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?He(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let 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t=e.getElementTypesInGroup("display"),n=a=>t.find(o=>o.name===a),r=a=>a&&Object.assign(Object.create(a),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Ji.map(a=>r(n(a)))].filter(a=>a!==void 0)}function Et(e){e.addTrackType(()=>{let t=(0,Uo.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,re.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new re.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,re.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Qi(e))n.addDisplayType(r);return n})}function Ft(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var pa=S(Se(),1),ma=S(qo(),1);var Qo=S(j(),1),ea=S(Jo(),1),Vt=S(X(),1);function ta(){return(0,Qo.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Vt.types.enumeration("LayoutMode",Le),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Vt.types.enumeration("ColorScheme",Pe),defaultValue:"auto"},...(0,ea.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var ia=S(Se(),1);var ke=S(j(),1),sa=S(J(),1),da=S(dn(),1),Dt=S(se(),1),ca=S(ra(),1),I=S(X(),1),Ze=S(aa(),1);var qe=S(sn(),1);var es=(0,ia.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-QF5OMTCH.js"));function ua(e){return I.types.compose("LinearGraphDisplay",sa.BaseDisplay,(0,ca.default)(),Ye(),I.types.model({type:I.types.literal("LinearGraphDisplay"),configuration:(0,ke.ConfigurationReference)(e),pane:I.types.maybe(I.types.frozen()),cutRegion:I.types.maybe(I.types.frozen()),coarseCut:I.types.optional(I.types.boolean,!1),maxRegionBp:I.types.optional(I.types.number,Xe),subgraphContext:I.types.optional(I.types.number,1),subgraphHaplotypes:I.types.maybe(I.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:a,...o}=n;return{...o,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,ke.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,ke.getConf)(t,"colorScheme")},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get chosenHaplotypes(){return t.subgraphHaplotypes??Wo(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${ne(n.end-n.start)}, max ${ne(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,Ze.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,Ze.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=Ke(Ue(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let a=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:a?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:a?"coarse":void 0,..._(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=St(n,t.capFor(r),_(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=_(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&mo(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=_(t.chosenLayoutMode);t.setLayoutMode(n);let a=_(n),o=t.host?He(t.host):void 0;return o&&!t.regionTooLarge&&(a.cutMargins!==r.cutMargins||a.wholeWalks!==r.wholeWalks)?t.recutAt(o):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,I.addDisposer)(t,(0,qe.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,a=n&&r?He(r):void 0;a&&t.settleOn(a)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?He(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let a=Math.floor(n.start),o=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:a,end:o},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,o-a),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Dt.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,da.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Be,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:sr,onClick:()=>{(0,Dt.getSession)(t).queueDialog(r=>[es,{model:t,open:!0,onClose:r}])}},...n]}}))}function Ht(e){e.addDisplayType(()=>{let t=ta();return Object.assign(new ma.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ua(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,pa.lazy)(()=>import("./chunks/LinearGraphDisplay-4CMVCEM5.js"))}),{adapterCapabilities:["getSubgraph"]})})}var ha=S(Ee(),1);var Ot=S(j(),1),la=S(X(),1);function Wt(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var ts=(0,Ot.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Ot.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:la.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Wt}),ga=ts;function _t(e){e.addAdapterType(()=>new ha.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Wt,configSchema:ga,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-NRDD66AK.js").then(t=>t.default)}))}var ka=S(Ee(),1);var Qe=S(j(),1),ya=S(X(),1);function ba(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function fa(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:ba(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:ba(`${t}.links.bed.gz`,n,r)}:e}function jt(e){let{coarse:t,baseUri:n}=e;return fa(typeof t=="object"&&t!==null?{...e,coarse:fa({baseUri:n,...t})}:e)}var Je=(e,t)=>(0,Qe.ConfigurationSchema)(e,{indexType:{model:ya.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ns=(0,Qe.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),rs=(0,Qe.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Je("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Je("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ns},{explicitlyTyped:!0,preProcessSnapshot:jt}),wa=rs;function $t(e){e.addAdapterType(()=>new ka.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:jt,configSchema:wa,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-NQEERXXI.js").then(t=>t.default)}))}var os=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function as(e){return"uri"in e?rn(e.uri).name:"localPath"in e?e.localPath:e.name}function is(e){return as(e).toLowerCase().endsWith(".gbz.db")}function ss(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function ds(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&is(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&on(e))return an({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function zt(e){e.addToExtensionPoint("Core-preProcessTrackConfig",ss),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,a)=>ds(n,r,a)??t(n,r,a)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>os.has(n)?"GraphTrack":t(n,r))}var Ra=S(se(),1),La=S(Fa(),1),Xt=S(Ea(),1),Ga=S(Da(),1);function oe(e){return typeof e=="object"&&e!==null}function xa(e){let t;if(oe(e)){let{refName:n,start:r,end:a,assemblyName:o}=e;typeof n=="string"&&typeof r=="number"&&typeof a=="number"&&(t={refName:n,start:r,end:a,assemblyName:typeof o=="string"?o:void 0})}return t}function cs(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Sa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function us(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>oe(n)&&Array.isArray(n.displays)?n.displays.filter(r=>oe(r)&&r.type==="LinearGraphDisplay"):[])}function Ma(e,t,n){let r=[],a=new Set(fe(e).map(o=>oe(o)?o.id:void 0));for(let o of e){if(oe(o)&&o.id===t)for(let i of us(o)){let s=xa(i.hoverHighlight);s&&Sa(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph-track",region:s})}if(oe(o)&&o.type==="GraphGenomeView"&&cs(o,t,a)){let i=xa(o.hoverHighlight);i&&Sa(i,n)&&r.push({key:typeof o.id=="string"?o.id:"graph",region:i})}}return r}var ae=S(de(),1),ps=(0,Ga.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,La.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),ms=(0,Xt.observer)(function({model:t,region:n}){let{classes:r}=ps(),a=t.getHighlightCoords(n);return a?(0,ae.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:a.left,width:a.width}}):null}),ls=(0,Xt.observer)(function({model:t}){let{views:n}=(0,Ra.getSession)(t);return(0,ae.jsx)(ae.Fragment,{children:Ma([...n],t.id,t.assemblyNames).map(({key:r,region:a})=>(0,ae.jsx)(ms,{model:t,region:a},`graph-hover-${r}`))})}),Ta=ls;var Aa=S(de(),1),gs="LinearGenomeView-TracksContainerComponent";function Yt(e){e.contributeToExtensionPoint(gs,({model:t})=>(0,Aa.jsx)(Ta,{model:t},"graphgenomeview-hover-highlight"))}var Na="GraphGenomeView";var Pa="4.0.21";var Ut=class extends Ia.default{constructor(){super(...arguments);this.name=Na;this.version=Pa}install(n){Bt(n),Ht(n),Et(n),Ft(n),Yt(n),$t(n),_t(n),pt(n),lt(n),zt(n),n.addRpcMethod(()=>new me(n)),n.addRpcMethod(()=>new pe(n)),n.addRpcMethod(()=>new ue(n))}configure(n){try{(0,va.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Be,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Ut as default};
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