jbrowse-plugin-graphgenomeviewer 4.3.0 → 4.4.1

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

@@ -1,7 +1,7 @@
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t?[t.reference,...t.rows].map((n,r)=>({label:n.label,y:r*20})):e.rowLabels},get fitPadLeft(){return Math.max(V,...this.drawnRowLabels.map(t=>sr(t.label,0).x1+6))},get genePins(){fe(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?mt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){fe(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||!this.drawsNodes||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return Bo(e.graph,e.bubbles,t,r=>n.get(r)??r,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?he(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return be(e.scale,e.pixelRows).scaleX},get scaleY(){return be(e.scale,e.pixelRows).scaleY},get axisScale(){return be(e.scale,e.pixelRows)},get layoutBounds(){let t=e.layoutResult,n=this.walkRowBars;return t?lt(t,{region:e.popStack.length===0?e.graphRegion:void 0,extent:n&&t.extent?Ue(n):void 0}):void 0}})).views(e=>({get geneTrack(){return dn(e.geneTrackChoices,e.geneTrackId)},get deletionEdgeIndexes(){return new Map(e.deletions.map(t=>[t.edgeIndex,t.bypassed]))},get hiddenEdgeIndexes(){return new Set(e.showDeletionEdges?[]:e.deletions.map(t=>t.edgeIndex))},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,r=n?.tubeMap?n.nodePositions:void 0,o=!1,a=!1;if(t&&e.drawnGraph)for(let i of e.drawnGraph.nodes)r&&!r[i.id]||(t.midpoints.has(i.id)?i.stable&&i.stable.rank>0&&(o=!0):a=!0);return{offReference:o,unplaced:a}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?Sa(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>dr(i,t.length)):t,r=new Set(e.hoveredRowWalks),o=e.drawnGraph?.paths;return n&&o&&r.size>0?n.map((a,i)=>r.has(o[i]?.name??"")?a:Mr):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:r}=e;return n&&r?je({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&&Vt(t.length)?Me(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}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?On(t):[];return t?io(t,{maxGap:n.length>0?jn(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,N.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,r=new Map(Object.entries(n??{}).map(([a,i])=>[i,a])),o=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>o(r.get(a))??o(a)},get geneTracksByAssembly(){let t=new Map;for(let n of(0,N.getSession)(e).tracks){let r=(0,ne.readConfObject)(n,"adapter").type;if(!wt.has(r))continue;let o={trackId:n.trackId,name:(0,ne.readConfObject)(n,"name"),adapterType:r};for(let a of(0,ne.readConfObject)(n,"assemblyNames")){let i=$e((0,N.getSession)(e),a);t.set(i,[...t.get(i)??[],o])}}return new Map([...t].flatMap(([n,r])=>{let o=dn(r,"");return o?[[n,o]]:[]}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars;if(!t||!e.showGenes)return;let n=[],r=0,o=0;for(let a of t.rows){if(!a.axis){o++;continue}let i=st(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,..._t(a.axis,a.bp)}})}return{reads:n.slice(0,ti),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-ti)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(20*e.scaleY)),a=[r.reference,...r.rows][o],i=o*20*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=Tr/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:st(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,..._t(r.axis,r.bp)}}},get walkRowGenes(){let t=e.walkRowBars;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?Nr([t.reference,...t.rows],n):void 0}})).views(e=>({get launchableAssemblies(){return so(ja(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Fe({views:[...(0,N.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),r=n?it(n):void 0,o=r?st(e.assemblyResolver,r):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,d=a&&i&&s?je({nodeId:t,nodeById:i,neighbors:s}):void 0,c=a&&d?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...d}:void 0;return{own:r&&o?{location:fn(r),assembly:o}:void 0,reference:a&&c?{location:fn(c),assembly:a.assemblyName}:void 0,highlight:a&&c?{location:c,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,N.getContainingView)(e)}catch{return}return Aa(t)?t:void 0}})).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=e.graph,n=t&&this.walkStripShown?Ye(t,e.graphRegion):void 0;return n?{...n,rows:ni(n.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(!t)return;let n=Math.max(...[t.reference,...t.rows].map(r=>r.label.length));return _r(t,{width:e.paneWidth,maxHeight:Fd,labelPx:n*6.2+16})},get cutsWholeWalks(){return Q(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?Wr(e.graph,[t.reference,...t.rows],r):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Xt(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&Q(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?kt(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Qr(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?Yr(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?Zr(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?Kr(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?no(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?jr(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?kt(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}=Xr(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=>br(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:Xt(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?zr(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return Td(e.darkMode?Za:Ja)},get referenceStripZonePx(){return e.referenceStripShown?Hr:0}})).views(e=>({get paneCeiling(){return Math.max(yn,e.paneHeight??Gd)},get fitPadTopBase(){let t=oo(e.tubeMapGenes);return V+Math.max(0,t-1)*ro+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=l=>(e.paneWidth-e.fitPadLeft-l)/t.w,s=l=>e.pixelRows?t.h+l+V<=a?1/0:0:(a-l-V)/t.h,d=Math.min(i(n+2*ge),s(o));return Math.min(i(V),s(o+r+ge))>=d?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ge:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(V,e.legendSize.width+2*ge):V},get minFitScale(){let t=e.layoutBounds,n=e.layoutResult,r=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&r&&!n.referenceAxis?Math.min(Nd/r,(this.paneCeiling-this.fitPadTop-V)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:r}=e.facet;return t===""?void 0:n.length===0&&r===void 0?t:{field:t,domain:[...n],...r===void 0?{}:{columns:r}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:r}=e.facet;return t?rt(t.map(o=>o.walks[0].name),e.hostPlacesX||n===""?"walk":n,r):void 0},facetGridIn(t){let n=this.facetPlacement,r=e.layoutBounds;return n&&r&&r.w>0?tt({count:n.count,bounds:r,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-V-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(yn,o.total);let a=Math.max(yn,e.legendSize.height+2*ge+e.referenceStripZonePx);return e.pixelRows?Math.min(r,Math.max(a,t.h+this.fitPadTop+V)):t.w>0&&n>0?Math.min(r,Math.max(a,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+V)):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?Ce(t,n.width,n.height,e.pixelRows,{padLeft:12,padTop:12,padRight:12,padBottom:12}):Ce(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 ta(kn(e),Ed)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,Id),n!==null&&n!==o&&a.set(n,ei),t.setNodeHighlights(a),t.setEdgeHighlight(r,ei)},paint(t){let n=(0,di.getDpr)();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?Za:Ja)}})).views(e=>({buildDrawing(t,n){let{nodePositions:r,graph:o,nodeById:a}=e;if(!r||!o||!a)return;fe(e.viewportDirty,e.positionsVersion);let i=(0,W.untracked)(()=>e.viewportToBuild());return{batch:at({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,W.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,deletions:e.deletionEdgeIndexes,deletionRoutes:e.deletionRoutes,hiddenEdges:e.hiddenEdgeIndexes,version:e.positionsVersion}),viewportBounds:i}},get overlayLabels(){return Sr(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?Vr(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=De(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?De(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:De(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(u=>r?.[u]??u),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:n.subgraphSnarls}}:void 0;if(!s)return;let d=e.showGenes?e.geneTrack:void 0,c=d?(0,N.getSession)(e).tracks.find(u=>u.trackId===d.trackId):void 0,l=c?(0,ne.expandTabixShorthand)((0,ne.readConfObject)(c,"adapter"),"gffGzLocation"):void 0,g=l?.type==="Gff3TabixAdapter"?{file:De(l.gffGzLocation),index:De(l.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(u=>u.color?u:u.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec: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:`${Q(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?la(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,spec:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?wa(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-V}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Ur(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?kt(r,o):void 0;return t&&n&&a?qr(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&&eo(o.yScale)?r.mismatches.filter(i=>to(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?ka(r,o,t,n):null)??Jr(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 r=$t(n,t);Wd(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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t=this.walkRowBars;return t?[t.reference,...t.rows].map((n,r)=>({label:n.label,y:r*20})):e.rowLabels},get fitPadLeft(){return Math.max($,...this.drawnRowLabels.map(t=>mr(t.label,0).x1+6))},get genePins(){ke(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?bt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){ke(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||!this.drawsNodes||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return $o(e.graph,e.bubbles,t,r=>n.get(r)??r,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?ye(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return we(e.scale,e.pixelRows).scaleX},get scaleY(){return we(e.scale,e.pixelRows).scaleY},get axisScale(){return we(e.scale,e.pixelRows)},get layoutBounds(){let t=e.layoutResult,n=this.walkRowBars;return t?ft(t,{region:e.popStack.length===0?e.graphRegion:void 0,extent:n&&t.extent?Je(n):void 0}):void 0}})).views(e=>({get geneTrack(){return ln(e.geneTrackChoices,e.geneTrackId)},get deletionEdgeIndexes(){return new Map(e.deletions.map(t=>[t.edgeIndex,t.bypassed]))},get hiddenEdgeIndexes(){return new Set(e.showDeletionEdges?[]:e.deletions.map(t=>t.edgeIndex))},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,r=n?.tubeMap?n.nodePositions:void 0,o=!1,a=!1;if(t&&e.drawnGraph)for(let i of e.drawnGraph.nodes)r&&!r[i.id]||(t.midpoints.has(i.id)?i.stable&&i.stable.rank>0&&(o=!0):a=!0);return{offReference:o,unplaced:a}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?La(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>lr(i,t.length)):t,r=new Set(e.hoveredRowWalks),o=e.drawnGraph?.paths;return n&&o&&r.size>0?n.map((a,i)=>r.has(o[i]?.name??"")?a:Pr):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&&_t(t.length)?Te(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}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?zn(t):[];return t?uo(t,{maxGap:n.length>0?Kn(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,v.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,r=new Map(Object.entries(n??{}).map(([a,i])=>[i,a])),o=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>o(r.get(a))??o(a)},get geneTracksByAssembly(){let t=new Map;for(let n of(0,v.getSession)(e).tracks){let r=(0,re.readConfObject)(n,"adapter").type;if(!St.has(r))continue;let o={trackId:n.trackId,name:(0,re.readConfObject)(n,"name"),adapterType:r};for(let a of(0,re.readConfObject)(n,"assemblyNames")){let i=We((0,v.getSession)(e),a);t.set(i,[...t.get(i)??[],o])}}return new Map([...t].flatMap(([n,r])=>{let o=ln(r,"");return o?[[n,o]]:[]}))}})).views(e=>({get launchableAssemblies(){return po(Ua(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Ve({views:[...(0,v.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),r=n?ut(n):void 0,o=r?pt(e.assemblyResolver,r):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,d=a&&i&&s?Ye({nodeId:t,nodeById:i,neighbors:s}):void 0,c=a&&d?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...d}:void 0;return{own:r&&o?{location:Sn(r),assembly:o}:void 0,reference:a&&c?{location:Sn(c),assembly:a.assemblyName}:void 0,highlight:a&&c?{location:c,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,v.getContainingView)(e)}catch{return}return Ca(t)?t:void 0}})).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=e.graph,n=t&&this.walkStripShown?qe(t,e.graphRegion):void 0;return n?{...n,rows:ii(n.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return ct(t,{width:e.paneWidth})},get cutsWholeWalks(){return ee(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?Br(e.graph,[t.reference,...t.rows],r):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:qt(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=pt(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...jt(a.axis,a.bp)}})}return{reads:n.slice(0,ai),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-ai)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(20*e.scaleY)),a=[r.reference,...r.rows][o],i=o*20*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=Ir/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:pt(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...jt(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?Cr([t.reference,...t.rows],n):void 0}})).views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&ee(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?Rt(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?no(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?qr(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?to(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?Zr(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?ao(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?Yr(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?Rt(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}=Ur(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=>xr(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:qt(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?Kr(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return Id(e.darkMode?ni:ti)},get referenceStripZonePx(){return e.referenceStripShown?zr:0}})).views(e=>({get paneCeiling(){return Math.max(Rn,e.paneHeight??vd)},get fitPadTopBase(){let t=so(e.tubeMapGenes);return $+Math.max(0,t-1)*io+e.referenceStripZonePx},get legendRoom(){let t=e.layoutBounds,{width:n,height:r}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let o=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=l=>(e.paneWidth-e.fitPadLeft-l)/t.w,s=l=>e.pixelRows?t.h+l+$<=a?1/0:0:(a-l-$)/t.h,d=Math.min(i(n+2*fe),s(o));return Math.min(i($),s(o+r+fe))>=d?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+fe:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max($,e.legendSize.width+2*fe):$},get minFitScale(){let t=e.layoutBounds,n=e.layoutResult,r=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&r&&!n.referenceAxis?Math.min(Cd/r,(this.paneCeiling-this.fitPadTop-$)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:r}=e.facet;return t===""?void 0:n.length===0&&r===void 0?t:{field:t,domain:[...n],...r===void 0?{}:{columns:r}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:r}=e.facet;return t?it(t.map(o=>o.walks[0].name),e.hostPlacesX||n===""?"walk":n,r):void 0},facetGridIn(t){let n=this.facetPlacement,r=e.layoutBounds;return n&&r&&r.w>0?ot({count:n.count,bounds:r,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-$-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(Rn,o.total);let a=Math.max(Rn,e.legendSize.height+2*fe+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?Ee(t,n.width,n.height,e.pixelRows,{padLeft:12,padTop:12,padRight:12,padBottom:12}):Ee(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 oa(Gn(e),Wd)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new 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Tr(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?Xr(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}-${t.end}`,a=Oe(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Oe(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:Oe(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(u=>r?.[u]??u),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let d=e.showGenes?e.geneTrack:void 0,c=d?(0,v.getSession)(e).tracks.find(u=>u.trackId===d.trackId):void 0,l=c?(0,re.expandTabixShorthand)((0,re.readConfObject)(c,"adapter"),"gffGzLocation"):void 0,g=l?.type==="Gff3TabixAdapter"?{file:Oe(l.gffGzLocation),index:Oe(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(u=>u.color?u:u.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,width:e.paneWidth,height:e.paneCeiling,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges||void 0}))},get figureUnavailable(){return e.layoutResult?e.drawsNodes||e.walkRowBars?void 0:`${ee(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?fa(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?Ra(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?Jr(t):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return 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r=e.layoutResult?.tubeMap,o=e.tubeMapFrame;return(r&&o?Ma(r,o,t,n):null)??eo(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 r=Wt(n,t);jd(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&&De([...(0,v.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,Y.addDisposer)(e,(0,gi.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!Q(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Hd=(0,fi.defineLaunchKeys)()({});function Rn(e){e.addViewType(()=>new bi.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Sn(),launchKeys:Hd,ReactComponent:(0,hi.lazy)(()=>import("./chunks/GraphGenomeView-ZB4N6Q3H.js"))}))}var yi=L(te(),1),we=L(de(),1),jd=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Xd(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"),...jd.map(o=>r(n(o)))].filter(o=>o!==void 0)}function Mn(e){e.addTrackType(()=>{let t=(0,yi.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,we.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new we.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,we.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Xd(e))n.addDisplayType(r);return n})}function Ln(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Ei=L(_e(),1),Fi=L(ki(),1);var Ri=L(te(),1),Mi=L(Si(),1),Gn=L(ie(),1);function Li(){return(0,Ri.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Gn.types.enumeration("LayoutMode",Ke),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Gn.types.enumeration("ColorScheme",Qe),defaultValue:"auto"},...(0,Mi.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Pi=L(_e(),1);var We=L(te(),1),vi=L(de(),1),Ci=L(Zn(),1),Tn=L(Se(),1),Ii=L(Ti(),1),E=L(ie(),1),vt=L(Ai(),1);var Ve=L(Ft(),1);var zd=(0,Pi.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-LXYUYPZS.js"));function Bi(e){return E.types.compose("LinearGraphDisplay",vi.BaseDisplay,(0,Ii.default)(),Nt(),E.types.model({type:E.types.literal("LinearGraphDisplay"),configuration:(0,We.ConfigurationReference)(e),pane:E.types.maybe(E.types.frozen()),cutRegion:E.types.maybe(E.types.frozen()),coarseCut:E.types.optional(E.types.boolean,!1),maxRegionBp:E.types.optional(E.types.number,Tt),subgraphContext:E.types.optional(E.types.number,1),subgraphHaplotypes:E.types.maybe(E.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,We.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,We.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??ui(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 (${ye(n.end-n.start)}, max ${ye(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,vt.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,vt.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=Pt(At(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,...Q(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=un(n,t.capFor(r),Q(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=Q(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&va(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=Q(t.chosenLayoutMode);t.setLayoutMode(n);let o=Q(n),a=t.host?xt(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,E.addDisposer)(t,(0,Ve.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,E.addDisposer)(t,(0,Ve.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,E.addDisposer)(t,(0,Ve.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,E.addDisposer)(t,(0,Ve.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?xt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?xt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,E.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,Tn.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Ci.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:ut,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:uo,onClick:()=>{(0,Tn.getSession)(t).queueDialog(r=>[zd,{model:t,open:!0,onClose:r}])}},...n]}}))}function Nn(e){e.addDisplayType(()=>{let t=Li();return Object.assign(new Fi.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Bi(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Ei.lazy)(()=>import("./chunks/LinearGraphDisplay-BCTYOYQ5.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Vi=L(pt(),1);var An=L(te(),1),$i=L(ie(),1);function Pn(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 Yd=(0,An.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,An.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:$i.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Pn}),Di=Yd;function vn(e){e.addAdapterType(()=>new Vi.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Pn,configSchema:Di,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CK7AE4QT.js").then(t=>t.default)}))}var ji=L(pt(),1);var It=L(te(),1),_i=L(ie(),1);function Wi(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Oi(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Wi(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Wi(`${t}.links.bed.gz`,n,r)}:e}function Cn(e){let{coarse:t,baseUri:n}=e;return Oi(typeof t=="object"&&t!==null?{...e,coarse:Oi({baseUri:n,...t})}:e)}var Ct=(e,t)=>(0,It.ConfigurationSchema)(e,{indexType:{model:_i.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Ud=(0,It.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ct("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ct("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Kd=(0,It.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ct("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ct("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Ud},{explicitlyTyped:!0,preProcessSnapshot:Cn}),Hi=Kd;function In(e){e.addAdapterType(()=>new ji.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Cn,configSchema:Hi,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-QPKEJZXA.js").then(t=>t.default)}))}var qd=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Jd(e){return Kn(e).toLowerCase().endsWith(".gbz.db")}function Zd(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 Qd(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Jd(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&qn(e))return Jn({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Bn(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Zd),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>Qd(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>qd.has(n)?"GraphTrack":t(n,r))}var Ui=L(Se(),1),Ki=L(ds(),1),En=L(ss(),1),qi=L(us(),1);function Xi(e){let t;if(Z(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 ec(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function zi(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function tc(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Z(n)&&Array.isArray(n.displays)?n.displays.filter(r=>Z(r)&&r.type==="LinearGraphDisplay"):[])}function Yi(e,t,n){let r=[],o=Ee(e),a=new Set(o.map(i=>Z(i)?i.id:void 0));for(let i of o){if(Z(i)&&i.id===t)for(let s of tc(i)){let d=Xi(s.hoverHighlight);d&&zi(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(Z(i)&&i.type==="GraphGenomeView"&&ec(i,t,a)){let s=Xi(i.hoverHighlight);s&&zi(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var ke=L(Re(),1),nc=(0,qi.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Ki.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),rc=(0,En.observer)(function({model:t,region:n}){let{classes:r}=nc(),o=t.getHighlightCoords(n);return o?(0,ke.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),oc=(0,En.observer)(function({model:t}){let{views:n}=(0,Ui.getSession)(t);return(0,ke.jsx)(ke.Fragment,{children:Yi([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,ke.jsx)(rc,{model:t,region:o},`graph-hover-${r}`))})}),Ji=oc;var Zi=L(Re(),1),ac="LinearGenomeView-TracksContainerComponent";function Fn(e){e.contributeToExtensionPoint(ac,({model:t})=>(0,Zi.jsx)(Ji,{model:t},"graphgenomeview-hover-highlight"))}var Qi="GraphGenomeView";var es="4.3.0";var $n=class extends ts.default{constructor(){super(...arguments);this.name=Qi;this.version=es}install(n){Rn(n),Nn(n),Mn(n),Ln(n),Fn(n),In(n),vn(n),Ut(n),qt(n),Bn(n),n.addRpcMethod(()=>new Ne(n)),n.addRpcMethod(()=>new Te(n)),n.addRpcMethod(()=>new Ge(n))}configure(n){try{(0,ns.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:ut,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{$n as default};
+`)&&(e.hoveredRowWalks=t)},setHoveredBubble(t){e.hoveredBubble=t},setPointerInPane(t){e.pointerInPane=t},setWalkStrip(t){e.walkStrip=t,e.stripHover=null},setStripHover(t){e.stripHover=t;let n=e.walkStripRows,r=e.walkStripFrame,o=t&&n?[n.reference,...n.rows].find(i=>i.name===t.row):void 0,a=o&&r&&e.graph?Er(e.graph,o,t.offset,r.scaleX):void 0;e.hoveredNode=a??null},setLegendSize(t){e.legendSize=t},setHoveredEdge(t){e.hoveredEdge=t},setSelectedNode(t){e.selectedNode=t},setDraggingNode(t){e.draggingNode=t},setPanning(t){e.isPanning=t},stopDragging(){e.draggingNode=null,e.isPanning=!1},clearInteractionState(){e.hoveredNode=null,e.hoveredBubble=null,e.hoveredEdge=null,e.selectedNode=null,e.draggingNode=null,e.isPanning=!1},showNodeDetails(t){let n=e.nodeById?.get(t),r=e.nodeById,o=e.nodeNeighbors;if(n&&r&&o){let a=(0,v.getSession)(e),i=e.graphRegion,s=i?Ye({nodeId:t,nodeById:r,neighbors:o}):void 0;(0,v.isSessionModelWithWidgets)(a)&&a.showWidget(a.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:ut(n)?.sample,contributingHaplotype:ut(n)?.haplotype,samples:n.samples?.join(", "),...i&&s?{refName:i.refName,assemblyName:i.assemblyName,start:s.start,end:s.end}:{}}}))}},setTransform(t,n,r){let{host:o}=e;e.viewportOwner==="host"&&o?o.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=Be(t),e.translateX=n),e.translateY=r},zoom(t,n,r){let{host:o}=e;if(e.viewportOwner==="host"&&o){o.zoomTo(o.bpPerPx/t,n);return}e.viewportOwner="user";let a=ia(e,t,n,r,e.pixelRows);e.scale=a.scale,e.translateX=a.translateX,e.translateY=a.translateY},setViewportDirty(){e.viewportRebuildPending=!1,e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){if(e.viewportOwner==="host"){let n=e.layoutBounds,r=e.facetGrid!==void 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e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,Y.addDisposer)(e,(0,yi.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!ee(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Yd=(0,xi.defineLaunchKeys)()({});function Nn(e){e.addViewType(()=>new ki.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Tn(),launchKeys:Yd,ReactComponent:(0,wi.lazy)(()=>import("./chunks/GraphGenomeView-QGJN2S27.js"))}))}var Si=M(ne(),1),Se=M(ue(),1),Ud=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Kd(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"),...Ud.map(o=>r(n(o)))].filter(o=>o!==void 0)}function Pn(e){e.addTrackType(()=>{let 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He=M(ne(),1),Ei=M(ue(),1),Fi=M(rr(),1),In=M(Ge(),1),$i=M(vi(),1),F=M(de(),1),Bt=M(Ci(),1);var _e=M(Vt(),1);var qd=(0,Bi.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-LXYUYPZS.js"));function Di(e){return F.types.compose("LinearGraphDisplay",Ei.BaseDisplay,(0,$i.default)(),vt(),F.types.model({type:F.types.literal("LinearGraphDisplay"),configuration:(0,He.ConfigurationReference)(e),pane:F.types.maybe(F.types.frozen()),cutRegion:F.types.maybe(F.types.frozen()),coarseCut:F.types.optional(F.types.boolean,!1),maxRegionBp:F.types.optional(F.types.number,At),subgraphContext:F.types.optional(F.types.number,1),subgraphHaplotypes:F.types.maybe(F.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,He.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,He.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??gi(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 (${xe(n.end-n.start)}, max ${xe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,Bt.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,Bt.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=Ct(It(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,...ee(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=hn(n,t.capFor(r),ee(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=ee(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ea(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=ee(t.chosenLayoutMode);t.setLayoutMode(n);let o=ee(n),a=t.host?Mt(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,F.addDisposer)(t,(0,_e.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,F.addDisposer)(t,(0,_e.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,F.addDisposer)(t,(0,_e.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,F.addDisposer)(t,(0,_e.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Mt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Mt(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,F.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,In.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Fi.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:gt,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:lo,onClick:()=>{(0,In.getSession)(t).queueDialog(r=>[qd,{model:t,open:!0,onClose:r}])}},...n]}}))}function Cn(e){e.addDisplayType(()=>{let t=Pi();return Object.assign(new Wi.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Di(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Vi.lazy)(()=>import("./chunks/LinearGraphDisplay-WPXUCJNR.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Hi=M(ht(),1);var Bn=M(ne(),1),Oi=M(de(),1);function En(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}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Jd=(0,Bn.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Bn.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Oi.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:En}),_i=Jd;function Fn(e){e.addAdapterType(()=>new Hi.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:En,configSchema:_i,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CK7AE4QT.js").then(t=>t.default)}))}var Ui=M(ht(),1);var Ft=M(ne(),1),zi=M(de(),1);function ji(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Xi(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:ji(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:ji(`${t}.links.bed.gz`,n,r)}:e}function $n(e){let{coarse:t,baseUri:n}=e;return Xi(typeof t=="object"&&t!==null?{...e,coarse:Xi({baseUri:n,...t})}:e)}var Et=(e,t)=>(0,Ft.ConfigurationSchema)(e,{indexType:{model:zi.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Zd=(0,Ft.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Et("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Et("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Qd=(0,Ft.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Et("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Et("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Zd},{explicitlyTyped:!0,preProcessSnapshot:$n}),Yi=Qd;function Dn(e){e.addAdapterType(()=>new Ui.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:$n,configSchema:Yi,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-QPKEJZXA.js").then(t=>t.default)}))}var ec=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function tc(e){return er(e).toLowerCase().endsWith(".gbz.db")}function nc(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 rc(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&tc(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&tr(e))return nr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Vn(e){e.addToExtensionPoint("Core-preProcessTrackConfig",nc),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>rc(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>ec.has(n)?"GraphTrack":t(n,r))}var Zi=M(Ge(),1),Qi=M(ms(),1),Wn=M(ps(),1),es=M(gs(),1);function Ki(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 oc(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function qi(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function ac(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 Ji(e,t,n){let r=[],o=De(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 ac(i)){let d=Ki(s.hoverHighlight);d&&qi(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(Q(i)&&i.type==="GraphGenomeView"&&oc(i,t,a)){let s=Ki(i.hoverHighlight);s&&qi(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Re=M(Le(),1),ic=(0,es.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Qi.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),sc=(0,Wn.observer)(function({model:t,region:n}){let{classes:r}=ic(),o=t.getHighlightCoords(n);return o?(0,Re.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),dc=(0,Wn.observer)(function({model:t}){let{views:n}=(0,Zi.getSession)(t);return(0,Re.jsx)(Re.Fragment,{children:Ji([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Re.jsx)(sc,{model:t,region:o},`graph-hover-${r}`))})}),ts=dc;var ns=M(Le(),1),cc="LinearGenomeView-TracksContainerComponent";function On(e){e.contributeToExtensionPoint(cc,({model:t})=>(0,ns.jsx)(ts,{model:t},"graphgenomeview-hover-highlight"))}var rs="GraphGenomeView";var os="4.4.1";var _n=class extends as.default{constructor(){super(...arguments);this.name=rs;this.version=os}install(n){Nn(n),Cn(n),Pn(n),An(n),On(n),Dn(n),Fn(n),Qt(n),tn(n),Vn(n),n.addRpcMethod(()=>new ve(n)),n.addRpcMethod(()=>new Ae(n)),n.addRpcMethod(()=>new Pe(n))}configure(n){try{(0,is.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:gt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{_n as default};
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