jbrowse-plugin-graphgenomeviewer 6.0.2 → 6.0.3

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

@@ -1,7 +1,7 @@
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e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?cr(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?he(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,ct.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,pe.getSession)(e).tracks.filter(n=>(0,ct.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,ct.readConfObject)(n,"name"),adapterType:(0,ct.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>it.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>hr.has(t.adapterType))},get repeatChoices(){return 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r=dt(e).filter(a=>Ld(a)).filter(a=>a.assemblyNames.includes(n));return r.find(a=>a.id===t)??(r.length===1?r[0]:void 0)}function ut(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Wi(e,t,n){n.catch(r=>{console.error(`[GraphGenomeView] ${t}`,r),e.notifyError?.(`${t}: ${r}`,r)})}var Td=1e3;function br(e,t=Td){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function Hi(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function ji({session:e,location:t,assembly:n,connectedViewId:r,tracks:o=[]}){let a=pt({views:e.views,connectedViewId:r,assemblyName:n}),i;return a?(Wi(e,`Could not show ${n} ${Ye(t)}`,Promise.resolve(a.navToLocString(Bt(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${Ye(t)}`,init:{assembly:n,loc:Bt(t),tracks:o}}).id,i}function Xi({session:e,location:t,assembly:n,connectedViewId:r}){let 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this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(le*e.scaleY)),a=[r.reference,...r.rows][o],i=o*le*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=To/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:ze(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...Mn(r.axis,r.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?vo([t.reference,...t.rows],n):void 0}}));var Ki=Ui.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&D(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(r=>r.refName===n.refName&&r.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?at(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Yo(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?Wo(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?ra(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?jo(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?qo(t,e.backboneGenes):[]},get 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a=e.bubbleHalos.find(i=>So(i.bubble,n));return{start:n.start,end:n.end,anchor:a?t(a.labelAt):void 0}}let r=e.hoveredNode??e.selectedNode,o=r===null?void 0:e.nodeSpan(r);return o&&r!==null?{...o,anchor:Et(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?na(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return Ja(e.darkMode?Ht:Wt)},get referenceStripZonePx(){return e.referenceStripShown?Qo:0}}));var Ji=Ki.views(e=>({get paneCeiling(){return Math.max(Ot,e.paneHeight??qa)},get fitPadTopBase(){let t=Zo(e.tubeMapGenes);return $+Math.max(0,t-1)*Jo+e.referenceStripZonePx},get legendRoom(){let t=e.layoutBounds,{width:n,height:r}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let o=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-e.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+$<=a?1/0:0:(a-m-$)/t.h,c=Math.min(i(n+2*Ne),s(o));return 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this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-$-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(Ot,o.total);let a=Math.max(Ot,e.legendSize.height+2*Ne+e.referenceStripZonePx);return e.pixelRows?Math.min(r,Math.max(a,t.h+this.fitPadTop+$)):t.w>0&&n>0?Math.min(r,Math.max(a,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+$)):r},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=e.layoutBounds,n=this.facetGrid;return t?n?Ge(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):Ge(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:e.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return On(tt(e),ai)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,ri),n!==null&&n!==o&&a.set(n,Yn),t.setNodeHighlights(a),t.setEdgeHighlight(r,Yn)},paint(t){let n=Co();t.updateTransform({scaleX:e.scaleX*n,scaleY:e.scaleY*n,translateX:e.translateX*n,translateY:e.translateY*n,dpr:n}),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?Ht:Wt)}})).views(e=>({buildDrawing(t,n){let{nodePositions:r,graph:o,nodeById:a}=e;if(!r||!o||!a)return;ue(e.viewportDirty,e.positionsVersion);let i=(0,yr.untracked)(()=>e.viewportToBuild());return{batch:Lt({nodePositions:e.walkRowBars?{}:r,graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:(0,yr.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,deletions:e.deletionEdgeIndexes,deletionRoutes:e.deletionRoutes,stranded:e.stranded,hiddenEdges:e.hiddenEdgeIndexes,version:e.positionsVersion}),viewportBounds:i}},get overlayLabels(){return Oo(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?Vo(t,r.id,r.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,r=n?.assemblyNameToPanSN,o=t&&`${t.refName}:${t.start}-${t.end}`,a=Ie(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ie(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:Ie(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(p=>r?.[p]??p),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let c=e.showGenes?e.geneTrack:void 0,d=c?(0,qi.getSession)(e).tracks.find(p=>p.trackId===c.trackId):void 0,m=d?(0,Zt.expandTabixShorthand)((0,Zt.readConfObject)(d,"adapter"),"gffGzLocation"):void 0,g=m?.type==="Gff3TabixAdapter"?{file:Ie(m.gffGzLocation),index:Ie(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges||void 0}))},get figureUnavailable(){return e.layoutResult?e.drawsNodes||e.walkRowBars?void 0:`${D(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base track or a GFA url":`bandage-figure draws no ${D(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?nr(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.colorDomain,fitToDrawing:e.popStack.length>0,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?rr(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-$}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Ho(t):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapReferenceNodes,n=e.tubeMapFrame,{host:r,graphRegion:o}=e,a=t&&n&&r?.initialized&&o?at(r,o):void 0;return t&&n&&a?Xo(t,i=>i*a.scale+a.translateX,n.x,e.paneWidth):[]}})).views(e=>({get tubeMapKeys(){let t=e.layoutResult,n=t?.tubeMap?.layout.reads??[],r=e.tubeMapPicture,o=e.tubeMapFrame,a=r&&o&&Uo(o.yScale)?r.mismatches.filter(i=>Ko(i,{x:o.x,width:e.paneWidth})):[];return{logWidths:t?.tubeMap!==void 0&&!t.referenceAxis,foldBp:e.tubeMapDeviations.length>0?e.tubeMapFold:void 0,forwardReads:n.some(i=>!i.is_reverse),reverseReads:n.some(i=>i.is_reverse),mismatches:new Set(a.map(i=>i.kind))}},tubeMapNodeAt(t,n){let r=e.layoutResult?.tubeMap,o=e.tubeMapFrame;return(r&&o?or(r,o,t,n):null)??zo(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));var Zi=Ji.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 r=Ve(n,t);ci(n,r),e.graph=r}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setShowReferenceStrip(t){e.showReferenceStrip=t},setTubeMapFold(t){e.tubeMapFold=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setWalkLayers(t){e.walkLayers=t},liftWalks(t){let n=new Map(e.walkLayers.map(r=>[r.walk,r]));e.walkLayers=t.map(r=>n.get(r)??{walk:r})},setFacet(t){t!==e.facet.field&&(e.facet.domain=[]),e.facet.field=t},setFacetColumns(t){e.facet.columns=t},toggleWalk(t){let 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e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?cr(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?he(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,ct.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,pe.getSession)(e).tracks.filter(n=>(0,ct.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,ct.readConfObject)(n,"name"),adapterType:(0,ct.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>it.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>hr.has(t.adapterType))},get repeatChoices(){return 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n&&o&&r.size>0?n.map((a,i)=>r.has(o[i]?.name??"")?a:mo):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:r}=e;return n&&r?ye({nodeId:t,nodeById:n,neighbors:r}):void 0}})).views(e=>({get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&wn(t.length)?Oe(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?e.nodeSpan(t):n?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return t&&n?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var fr=w(U(),1);function Q(e){return typeof e=="object"&&e!==null}function Td(e){return Q(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function dt(e){return e.flatMap(t=>Q(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function pt({views:e,connectedViewId:t,assemblyName:n}){let r=dt(e).filter(a=>Td(a)).filter(a=>a.assemblyNames.includes(n));return r.find(a=>a.id===t)??(r.length===1?r[0]:void 0)}function ut(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Hi(e,t,n){n.catch(r=>{console.error(`[GraphGenomeView] ${t}`,r),e.notifyError?.(`${t}: ${r}`,r)})}var vd=1e3;function br(e,t=vd){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function ji(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function Xi({session:e,location:t,assembly:n,connectedViewId:r,tracks:o=[]}){let a=pt({views:e.views,connectedViewId:r,assemblyName:n}),i;return a?(Hi(e,`Could not show ${n} ${Ye(t)}`,Promise.resolve(a.navToLocString(Bt(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${Ye(t)}`,init:{assembly:n,loc:Bt(t),tracks:o}}).id,i}function zi({session:e,location:t,assembly:n,connectedViewId:r}){let 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n=e.nodeById?.get(t),r=n?Xe(n):void 0,o=r?ze(e.assemblyResolver,r):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,c=a&&i&&s?ye({nodeId:t,nodeById:i,neighbors:s}):void 0,d=a&&c?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...c}:void 0;return{own:r&&o?{location:br(r),assembly:o}:void 0,reference:a&&d?{location:br(d),assembly:a.assemblyName}:void 0,highlight:a&&d?{location:d,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,Le.getContainingView)(e)}catch{return}return vi(t)?t:void 0}}));var Ki=Ui.views(e=>({get walkStripShown(){return e.walkStrip&&!e.host&&e.modeDrawsNodes&&!e.layoutResult?.tubeMap&&!e.walkRowBars&&e.popStack.length===0&&(e.graph?.paths?.length??0)>1},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:He(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ct(t,{width:e.paneWidth})},get cutsWholeWalks(){return _(e.chosenLayoutMode).wholeWalks||e.walkStrip&&!e.host},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,r=n===null?void 0:e.nodeById?.get(n);return t&&r&&e.graph?Ao(e.graph,[t.reference,...t.rows],r):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Et(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],r=0,o=0;for(let a of t.rows){if(!a.axis){o++;continue}let i=ze(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...Mn(a.axis,a.bp)}})}return{reads:n.slice(0,Un),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-Un)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(le*e.scaleY)),a=[r.reference,...r.rows][o],i=o*le*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=To/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:ze(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...Mn(r.axis,r.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?vo([t.reference,...t.rows],n):void 0}}));var qi=Ki.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&_(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(r=>r.refName===n.refName&&r.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?at(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Yo(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?Wo(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?ra(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?jo(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?qo(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;return e.showReferenceStrip&&e.referenceStripApplies&&t?ea(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?at(t,n):void 0}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.referenceStripFrame!==void 0},get referenceStripOverhangs(){let t=e.referenceStripFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:r}=ta(e.referenceStripBlocks,t,e.paneWidth);return n>0||r>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=a=>({x:a.x*e.scaleX+e.translateX,y:a.y*e.scaleY+e.translateY}),n=e.hoveredNode===null?e.hoveredBubble:null;if(n){let a=e.bubbleHalos.find(i=>So(i.bubble,n));return{start:n.start,end:n.end,anchor:a?t(a.labelAt):void 0}}let r=e.hoveredNode??e.selectedNode,o=r===null?void 0:e.nodeSpan(r);return o&&r!==null?{...o,anchor:Et(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?na(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return Za(e.darkMode?Ht:Wt)},get referenceStripZonePx(){return e.referenceStripShown?Qo:0}}));var Zi=qi.views(e=>({get paneCeiling(){return Math.max(Ot,e.paneHeight??Ja)},get fitPadTopBase(){let t=Zo(e.tubeMapGenes);return $+Math.max(0,t-1)*Jo+e.referenceStripZonePx},get legendRoom(){let t=e.layoutBounds,{width:n,height:r}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let o=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-e.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+$<=a?1/0:0:(a-m-$)/t.h,c=Math.min(i(n+2*Ne),s(o));return 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this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-$-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(Ot,o.total);let a=Math.max(Ot,e.legendSize.height+2*Ne+e.referenceStripZonePx);return e.pixelRows?Math.min(r,Math.max(a,t.h+this.fitPadTop+$)):t.w>0&&n>0?Math.min(r,Math.max(a,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+$)):r},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=e.layoutBounds,n=this.facetGrid;return t?n?Ge(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):Ge(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:e.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return On(tt(e),ii)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,oi),n!==null&&n!==o&&a.set(n,Yn),t.setNodeHighlights(a),t.setEdgeHighlight(r,Yn)},paint(t){let n=Io();t.updateTransform({scaleX:e.scaleX*n,scaleY:e.scaleY*n,translateX:e.translateX*n,translateY:e.translateY*n,dpr:n}),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?Ht:Wt)}})).views(e=>({buildDrawing(t,n){let{nodePositions:r,graph:o,nodeById:a}=e;if(!r||!o||!a)return;ue(e.viewportDirty,e.positionsVersion);let i=(0,yr.untracked)(()=>e.viewportToBuild());return{batch:Lt({nodePositions:e.walkRowBars?{}:r,graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:(0,yr.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,deletions:e.deletionEdgeIndexes,deletionRoutes:e.deletionRoutes,stranded:e.stranded,hiddenEdges:e.hiddenEdgeIndexes,version:e.positionsVersion}),viewportBounds:i}},get overlayLabels(){return Oo(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?Do(t,r.id,r.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,r=n?.assemblyNameToPanSN,o=t&&`${t.refName}:${t.start}-${t.end}`,a=Ce(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ce(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:Ce(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(p=>r?.[p]??p),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let c=e.showGenes?e.geneTrack:void 0,d=c?(0,Ji.getSession)(e).tracks.find(p=>p.trackId===c.trackId):void 0,m=d?(0,Zt.expandTabixShorthand)((0,Zt.readConfObject)(d,"adapter"),"gffGzLocation"):void 0,g=m?.type==="Gff3TabixAdapter"?{file:Ce(m.gffGzLocation),index:Ce(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges||void 0}))},get figureUnavailable(){return e.layoutResult?e.drawsNodes||e.walkRowBars?void 0:`${_(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base track or a GFA url":`bandage-figure draws no ${_(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?nr(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.colorDomain,fitToDrawing:e.popStack.length>0,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?rr(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-$}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Ho(t):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapReferenceNodes,n=e.tubeMapFrame,{host:r,graphRegion:o}=e,a=t&&n&&r?.initialized&&o?at(r,o):void 0;return t&&n&&a?Xo(t,i=>i*a.scale+a.translateX,n.x,e.paneWidth):[]}})).views(e=>({get tubeMapKeys(){let t=e.layoutResult,n=t?.tubeMap?.layout.reads??[],r=e.tubeMapPicture,o=e.tubeMapFrame,a=r&&o&&Uo(o.yScale)?r.mismatches.filter(i=>Ko(i,{x:o.x,width:e.paneWidth})):[];return{logWidths:t?.tubeMap!==void 0&&!t.referenceAxis,foldBp:e.tubeMapDeviations.length>0?e.tubeMapFold:void 0,forwardReads:n.some(i=>!i.is_reverse),reverseReads:n.some(i=>i.is_reverse),mismatches:new Set(a.map(i=>i.kind))}},tubeMapNodeAt(t,n){let r=e.layoutResult?.tubeMap,o=e.tubeMapFrame;return(r&&o?or(r,o,t,n):null)??zo(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));var Qi=Zi.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 r=De(n,t);di(n,r),e.graph=r}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setShowReferenceStrip(t){e.showReferenceStrip=t},setTubeMapFold(t){e.tubeMapFold=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setWalkLayers(t){e.walkLayers=t},liftWalks(t){let n=new Map(e.walkLayers.map(r=>[r.walk,r]));e.walkLayers=t.map(r=>n.get(r)??{walk:r})},setFacet(t){t!==e.facet.field&&(e.facet.domain=[]),e.facet.field=t},setFacetColumns(t){e.facet.columns=t},toggleWalk(t){let n=e.walkLayers;e.walkLayers=n.some(r=>r.walk===t)?n.filter(r=>r.walk!==t):[...n,{walk:t}]},setWalkColor(t,n){e.walkLayers=e.walkLayers.map(r=>r.walk===t?{...r,color:{...r.color,...n}}:r)},setPaneHeight(t){e.paneHeight=t},setWalkRowSamples(t){e.walkRowSamples=t},pairWithLinearView(t){let n=e.connectedViewId;n!==void 0&&dt([...(0,mt.getSession)(e).views]).some(o=>o.id===n)||(e.connectedViewId=t)},setHoveredNode(t){e.hoveredNode=t},setHoveredRowWalks(t){t.join(`
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e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,X.addDisposer)(e,(0,ys.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!D(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Vd=(0,xs.defineLaunchKeys)()({});function Sr(e){e.addViewType(()=>new ks.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:xr(),launchKeys:Vd,ReactComponent:(0,ws.lazy)(()=>import("./chunks/GraphGenomeView-QAJUST4R.js"))}))}var Ss=w(U(),1),Ee=w(ge(),1),Rr=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function _d(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Rr.map(o=>r(n(o)))].filter(o=>o!==void 0)}function Mr(e){e.addTrackType(()=>{let t=(0,Ss.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ee.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ee.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ee.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of _d(e))n.addDisplayType(r);return n})}function Lr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Os=w($e(),1),Ws=w(Ms(),1);var vs=w(U(),1),As=w(Ts(),1),Tr=w(re(),1);function Ns(){return(0,vs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Tr.types.enumeration("LayoutMode",xt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Tr.types.enumeration("ColorScheme",St),defaultValue:"auto"},...(0,As.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Fs=w($e(),1);var gt=w(U(),1),$s=w(ge(),1),Vs=w(qr(),1),vr=w(ae(),1),_s=w(Gs(),1),I=w(re(),1),an=w(Is(),1);var lt=w(bt(),1);function Es(e){return e instanceof Error&&(e.name==="NodeLimitError"||e.regionTooLarge===!0||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Bs(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var Dd=(0,Fs.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-CLI6V424.js"));function Ds(e){return I.types.compose("LinearGraphDisplay",$s.BaseDisplay,(0,_s.default)(),nn(),I.types.model({type:I.types.literal("LinearGraphDisplay"),configuration:(0,gt.ConfigurationReference)(e),pane:I.types.maybe(I.types.frozen()),overviewRowsChoice:I.types.maybe(I.types.frozen()),overviewRowOrder: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,et),subgraphContext:I.types.optional(I.types.number,1),subgraphHaplotypes:I.types.maybe(I.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:r,overviewRowOrder:o,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0})).views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,gt.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,gt.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??hs(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 (${Se(n.end-n.start)}, max ${Se(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,an.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,an.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,t.dense=void 0},setDense(n){t.dense=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=on(rn(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0,...D(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=ar(n,t.capFor(r),D(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=D(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||Bs(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ai(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,I.isAlive)(t)&&Es(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=D(t.chosenLayoutMode);t.setLayoutMode(n);let o=D(n),a=t.host?zt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):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,lt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,lt.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,lt.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,I.addDisposer)(t,(0,lt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?zt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?zt(t.host):void 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Od=(0,Nr.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Nr.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Hs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Pr}),js=Od;function Gr(e){e.addAdapterType(()=>new Xs.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Pr,configSchema:js,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-5AQXW2NH.js").then(t=>t.default)}))}var qs=w(Vt(),1);var cn=w(U(),1),Us=w(re(),1);function zs(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Ys(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:zs(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:zs(`${t}.links.bed.gz`,n,r)}:e}function Cr(e){let{coarse:t,baseUri:n}=e;return Ys(typeof t=="object"&&t!==null?{...e,coarse:Ys({baseUri:n,...t})}:e)}var sn=(e,t)=>(0,cn.ConfigurationSchema)(e,{indexType:{model:Us.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Wd=(0,cn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Hd=(0,cn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Wd},{explicitlyTyped:!0,preProcessSnapshot:Cr}),Ks=Hd;function 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t=e.walkChoices;return[{label:"Layout",subMenu:io.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,onClick:()=>{e.switchLayout(n.value)}}))},{label:"Color",subMenu:co.map(n=>({type:"radio",label:n.label,checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},...t.length>0&&e.liftsWalks?[{label:"Walk",subMenu:[{label:"None",onClick:()=>{e.setWalkLayers([])}},...e.walkLayers.length>1&&e.modeDrawsNodes?[{label:"Side by side",subMenu:ti.map(({value:n,label:r})=>({type:"radio",label:r,checked:e.facet.field===n,onClick:()=>{e.setFacet(n)}}))}]:[],...e.facetPanels&&e.facet.field==="walk"&&!e.hostPlacesX?[{label:"Columns",subMenu:[void 0,...e.facetPanels.map((n,r)=>r+1)].map(n=>({type:"radio",label:n===void 0?"Auto":`${n}`,checked:e.facet.columns===n,onClick:()=>{e.setFacetColumns(n)}}))}]:[],...t.length>zn?[{label:"Choose 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Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(o=>{r.notify(`Could not copy the figure spec: ${String(o)}`)})}}]},launchMenuItems(){let t=[];for(let n of sa({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:r=>{e.showInLinearView(r)},onShowSynteny:r=>{e.showSyntenyView(r)}}))(0,ls.pushLaunchViewMenuItem)(t,n);return t}}));function nn(){return gs}var kr=w(U(),1);function hs(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function fs(e){let t=(0,kr.readConfObject)(e,"assemblyNames"),n=hs(t)?t.slice(1):[];return n.length>0?n:void 0}function rn(e){let t=(0,kr.readConfObject)(e,"assemblyNames");return hs(t)?t[0]:void 0}function on(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function Dd(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function xr(){return X.types.compose("GraphGenomeView",bs.BaseViewModel,nn(),X.types.model({type:X.types.literal("GraphGenomeView"),gfaLocation:X.types.maybe(X.types.frozen()),loadedRegion:X.types.maybe(X.types.frozen()),loadedTrackId:X.types.optional(X.types.string,""),subgraphContext:X.types.optional(X.types.number,1),subgraphHaplotypes:X.types.maybe(X.types.frozen()),maxRegionBp:X.types.optional(X.types.number,et)})).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,ys.getSession)(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return e.launchMenuItems()}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(Dd(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let r=e.sourceTrack,o=n.end-n.start,a=r?on(rn(r),n.assemblyName):void 0;if(!r)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(o>e.maxRegionBp)e.setError(new Error(`Region too large (${Se(o)}) \u2014 zoom in to view graph (max ${Se(e.maxRegionBp)})`));else return e.cutSubgraph(he(e,r),n,{hops:e.subgraphContext,haplotypes:e.subgraphHaplotypes,...e.cutsWholeWalks?{snarls:"overlapping"}:{}})}}}).actions(e=>({retryLoad(){e.load()},switchLayout(t){let n=e.cutsWholeWalks;return e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,X.addDisposer)(e,(0,ws.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!_(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Vd=(0,Ss.defineLaunchKeys)()({});function Sr(e){e.addViewType(()=>new xs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:xr(),launchKeys:Vd,ReactComponent:(0,ks.lazy)(()=>import("./chunks/GraphGenomeView-PTYYXWL7.js"))}))}var Rs=w(U(),1),Ee=w(ge(),1),Rr=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function _d(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Rr.map(o=>r(n(o)))].filter(o=>o!==void 0)}function Mr(e){e.addTrackType(()=>{let t=(0,Rs.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ee.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ee.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ee.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of _d(e))n.addDisplayType(r);return n})}function Lr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Ws=w($e(),1),Hs=w(Ls(),1);var As=w(U(),1),Ns=w(vs(),1),Tr=w(re(),1);function Ps(){return(0,As.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Tr.types.enumeration("LayoutMode",xt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Tr.types.enumeration("ColorScheme",St),defaultValue:"auto"},...(0,Ns.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var $s=w($e(),1);var gt=w(U(),1),Ds=w(ge(),1),Vs=w(qr(),1),vr=w(ae(),1),_s=w(Is(),1),C=w(re(),1),an=w(Es(),1);var lt=w(bt(),1);function Bs(e){return e instanceof Error&&(e.name==="NodeLimitError"||e.regionTooLarge===!0||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Fs(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var Od=(0,$s.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-DCV2WZXB.js"));function Os(e){return C.types.compose("LinearGraphDisplay",Ds.BaseDisplay,(0,_s.default)(),nn(),C.types.model({type:C.types.literal("LinearGraphDisplay"),configuration:(0,gt.ConfigurationReference)(e),pane:C.types.maybe(C.types.frozen()),overviewRowsChoice:C.types.maybe(C.types.frozen()),overviewRowOrder:C.types.maybe(C.types.frozen()),cutRegion:C.types.maybe(C.types.frozen()),coarseCut:C.types.optional(C.types.boolean,!1),maxRegionBp:C.types.optional(C.types.number,et),subgraphContext:C.types.optional(C.types.number,1),subgraphHaplotypes:C.types.maybe(C.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:r,overviewRowOrder:o,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0})).views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,gt.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,gt.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??fs(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${Se(n.end-n.start)}, max ${Se(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,an.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,an.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,t.dense=void 0},setDense(n){t.dense=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=on(rn(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"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=ar(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||Fs(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ni(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,C.isAlive)(t)&&Bs(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=_(t.chosenLayoutMode);t.setLayoutMode(n);let o=_(n),a=t.host?zt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):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,C.addDisposer)(t,(0,lt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,C.addDisposer)(t,(0,lt.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,C.addDisposer)(t,(0,lt.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,C.addDisposer)(t,(0,lt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?zt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?zt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,C.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,vr.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Vs.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:$t,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a 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Wd=(0,Nr.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Nr.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:js.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:Pr}),Xs=Wd;function Gr(e){e.addAdapterType(()=>new zs.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Pr,configSchema:Xs,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-JKMI26BD.js").then(t=>t.default)}))}var Js=w(Dt(),1);var cn=w(U(),1),Ks=w(re(),1);function Ys(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Us(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Ys(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Ys(`${t}.links.bed.gz`,n,r)}:e}function Ir(e){let{coarse:t,baseUri:n}=e;return Us(typeof t=="object"&&t!==null?{...e,coarse:Us({baseUri:n,...t})}:e)}var sn=(e,t)=>(0,cn.ConfigurationSchema)(e,{indexType:{model:Ks.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Hd=(0,cn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),jd=(0,cn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Hd},{explicitlyTyped:!0,preProcessSnapshot:Ir}),qs=jd;function Cr(e){e.addAdapterType(()=>new Js.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Ir,configSchema:qs,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-CNC5EQ2T.js").then(t=>t.default)}))}var Xd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function zd(e){return Yr(e).toLowerCase().endsWith(".gbz.db")}function Yd(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 Ud(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&zd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Ur(e))return Kr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Er(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Yd),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>Ud(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Xd.has(n)?"GraphTrack":t(n,r))}var tc=w(ae(),1),nc=w(bc(),1),Br=w(fc(),1),rc=w(yc(),1);function Zs(e){let t;if(Q(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Kd(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Qs(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function qd(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(r=>Q(r)&&r.type==="LinearGraphDisplay"):[])}function ec(e,t,n){let r=[],o=dt(e),a=new Set(o.map(i=>Q(i)?i.id:void 0));for(let i of o){if(Q(i)&&i.id===t)for(let s of qd(i)){let c=Zs(s.hoverHighlight);c&&Qs(c,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&Kd(i,t,a)){let s=Zs(i.hoverHighlight);s&&Qs(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Be=w(Fe(),1),Jd=(0,rc.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,nc.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),Zd=(0,Br.observer)(function({model:t,region:n}){let{classes:r}=Jd(),o=t.getHighlightCoords(n);return o?(0,Be.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Qd=(0,Br.observer)(function({model:t}){let{views:n}=(0,tc.getSession)(t);return(0,Be.jsx)(Be.Fragment,{children:ec([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Be.jsx)(Zd,{model:t,region:o},`graph-hover-${r}`))})}),oc=Qd;var ac=w(Fe(),1),ep="LinearGenomeView-TracksContainerComponent";function Fr(e){e.contributeToExtensionPoint(ep,({model:t})=>(0,ac.jsx)(oc,{model:t},"graphgenomeview-hover-highlight"))}var ic=w(ge(),1);function tp(e){return e.views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)}}))}function $r(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof ic.DisplayType&&Rr.includes(t.name)&&t.extendStateModel(tp),t))}var sc="GraphGenomeView";var cc="6.0.3";var Dr=class extends dc.default{constructor(){super(...arguments);this.name=sc;this.version=cc}install(n){Sr(n),Ar(n),Mr(n),Lr(n),Fr(n),Cr(n),Gr(n),Gn(n),Cn(n),Er(n),$r(n),n.addRpcMethod(()=>new qe(n)),n.addRpcMethod(()=>new Ke(n)),n.addRpcMethod(()=>new Ue(n))}configure(n){try{(0,pc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:$t,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{Dr as default};
 //# sourceMappingURL=jbrowse-plugin-graphgenomeviewer.esm.js.map