npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 5.1.0 → 5.2.0 - Mend

jbrowse-plugin-graphgenomeviewer 5.1.0 → 5.2.0

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

@@ -1,7 +1,7 @@
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Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?uo([t.reference,...t.rows],n):void 0}}));var zi=Xi.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&V(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?_e(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Lo(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?So(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?$o(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?Mo(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?Po(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?Bo(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?_e(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}=Fo(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=>ao(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:It(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?Oo(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return _a(e.darkMode?Ht:Wt)},get referenceStripZonePx(){return e.referenceStripShown?Eo:0}}));var Ki=zi.views(e=>({get paneCeiling(){return Math.max(_t,e.paneHeight??Va)},get fitPadTopBase(){let t=Co(e.tubeMapGenes);return $+Math.max(0,t-1)*No+e.referenceStripZonePx},get legendRoom(){let t=e.layoutBounds,{width:n,height:r}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let o=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-e.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+$<=a?1/0:0:(a-m-$)/t.h,d=Math.min(i(n+2*Ae),s(o));return Math.min(i($),s(o+r+Ae))>=d?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+Ae:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max($,e.legendSize.width+2*Ae):$},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(Wa/r,(this.paneCeiling-this.fitPadTop-$)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:r}=e.facet;return t===""?void 0:n.length===0&&r===void 0?t:{field:t,domain:[...n],...r===void 0?{}:{columns:r}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:r}=e.facet;return t?Gt(t.map(o=>o.walks[0].name),e.hostPlacesX||n===""?"walk":n,r):void 0},facetGridIn(t){let n=this.facetPlacement,r=e.layoutBounds;return n&&r&&r.w>0?Mt({count:n.count,bounds:r,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-$-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(_t,o.total);let a=Math.max(_t,e.legendSize.height+2*Ae+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?Ze(t,n.width,n.height,e.pixelRows,{padLeft:12,padTop:12,padRight:12,padBottom:12}):Ze(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 Na(et(e),Ka)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,Ya),n!==null&&n!==o&&a.set(n,En),t.setNodeHighlights(a),t.setEdgeHighlight(r,En)},paint(t){let n=(0,Ui.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?Ht:Wt)}})).views(e=>({buildDrawing(t,n){let{nodePositions:r,graph:o,nodeById:a}=e;if(!r||!o||!a)return;le(e.viewportDirty,e.positionsVersion);let i=(0,Kn.untracked)(()=>e.viewportToBuild());return{batch:St({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,Kn.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 bo(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?xo(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}-${t.end}`,a=Ne(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ne(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:Ne(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(p=>r?.[p]??p),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let d=e.showGenes?e.geneTrack:void 0,c=d?(0,Yi.getSession)(e).tracks.find(p=>p.trackId===d.trackId):void 0,m=c?(0,Qt.expandTabixShorthand)((0,Qt.readConfObject)(c,"adapter"),"gffGzLocation"):void 0,g=m?.type==="Gff3TabixAdapter"?{file:Ne(m.gffGzLocation),index:Ne(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges||void 0}))},get figureUnavailable(){return e.layoutResult?e.drawsNodes||e.walkRowBars?void 0:`${V(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 ${V(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?wi(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.colorDomain,fitToDrawing:e.popStack.length>0,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?Si(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-$}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Ro(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?_e(r,o):void 0;return t&&n&&a?vo(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&&Ao(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?Ri(r,o,t,n):null)??Go(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));var qi=Ki.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=lt(n,t);Za(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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o=Di(e,r),a=Di(e,n),i=t.filter(c=>a.includes(c.sample)),s=i.length>=2?i:t,d={init:{views:s.map(c=>({assembly:c.sample,loc:Tt(c),...r!==void 0&&o.includes(c.sample)?{tracks:[r]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?Vi(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",d)):e.addView("LinearSyntenyView",d)}var ji=$i.views(e=>({get contributingAssemblies(){let t=e.graph,n=t?yr(t):[];return t?_o(t,{maxGap:n.length>0?xr(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,xe.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,r=new Map(Object.entries(n??{}).map(([a,i])=>[i,a])),o=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>o(r.get(a))??o(a)},get geneTracksByAssembly(){let t=new Map;for(let n of(0,xe.getSession)(e).tracks){let r=(0,Yt.readConfObject)(n,"adapter").type;if(!qe.has(r))continue;let o={trackId:n.trackId,name:(0,Yt.readConfObject)(n,"name"),adapterType:r};for(let a 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t;try{t=(0,xe.getContainingView)(e)}catch{return}return bi(t)?t:void 0}}));var Xi=ji.views(e=>({get walkStripShown(){return e.walkStrip&&!e.host&&e.modeDrawsNodes&&!e.layoutResult?.tubeMap&&!e.walkRowBars&&e.popStack.length===0&&(e.graph?.paths?.length??0)>1},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:mt(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Lt(t,{width:e.paneWidth})},get cutsWholeWalks(){return _(e.chosenLayoutMode).wholeWalks||e.walkStrip&&!e.host},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,r=n===null?void 0:e.nodeById?.get(n);return t&&r&&e.graph?po(e.graph,[t.reference,...t.rows],r):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Gt(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],r=0,o=0;for(let a of t.rows){if(!a.axis){o++;continue}let i=De(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...un(a.axis,a.bp)}})}return{reads:n.slice(0,Pn),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-Pn)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(20*e.scaleY)),a=[r.reference,...r.rows][o],i=o*20*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=so/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:De(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...un(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?co([t.reference,...t.rows],n):void 0}}));var zi=Xi.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?Ke(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Ao(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?Ro(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?Do(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?Lo(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?vo(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?Eo(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?Ke(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}=Fo(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=>ro(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:Gt(e.nodePositions?.[r],t)}:void 0},referenceStripNodeAt(t,n){let r=e.referenceStripFrame;return e.referenceStripShown&&r?$o(e.referenceStripBlocks,r,t,n):void 0},get paperCss(){return $a(e.darkMode?Et:Bt)},get referenceStripZonePx(){return e.referenceStripShown?Bo:0}}));var Ki=zi.views(e=>({get paneCeiling(){return Math.max(It,e.paneHeight??Fa)},get fitPadTopBase(){let t=Io(e.tubeMapGenes);return $+Math.max(0,t-1)*Co+e.referenceStripZonePx},get legendRoom(){let t=e.layoutBounds,{width:n,height:r}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let o=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-e.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+$<=a?1/0:0:(a-m-$)/t.h,d=Math.min(i(n+2*Te),s(o));return Math.min(i($),s(o+r+Te))>=d?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+Te:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max($,e.legendSize.width+2*Te):$},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(Da/r,(this.paneCeiling-this.fitPadTop-$)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:r}=e.facet;return t===""?void 0:n.length===0&&r===void 0?t:{field:t,domain:[...n],...r===void 0?{}:{columns:r}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:r}=e.facet;return t?St(t.map(o=>o.walks[0].name),e.hostPlacesX||n===""?"walk":n,r):void 0},facetGridIn(t){let n=this.facetPlacement,r=e.layoutBounds;return n&&r&&r.w>0?kt({count:n.count,bounds:r,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=e.layoutBounds,n=e.paneWidth-$-this.fitPadRight,r=this.paneCeiling;if(!t)return r;let o=this.facetGrid;if(o)return Math.max(It,o.total);let a=Math.max(It,e.legendSize.height+2*Te+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?ze(t,n.width,n.height,e.pixelRows,{padLeft:12,padTop:12,padRight:12,padBottom:12}):ze(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(Ue(e),Xa)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:r,selectedNode:o}=e,a=new Map;o!==null&&a.set(o,Ha),n!==null&&n!==o&&a.set(n,Nn),t.setNodeHighlights(a),t.setEdgeHighlight(r,Nn)},paint(t){let n=(0,Ui.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?Et:Bt)}})).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,Yn.untracked)(()=>e.viewportToBuild());return{batch:yt({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,Yn.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 yo(e)},hoveredOn(t){let n=e.hoveredNode,r=n?e.nodeById?.get(n):void 0;return r?So(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}-${t.end}`,a=Pe(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Pe(n.gbzDbLocation):void 0,s=a?{gfa:a,region:o}:i&&t&&o?{gbz:{db:i,index:Pe(n.haplotypeIndexLocation),region:o,haplotypes:e.cutHaplotypes?.map(p=>r?.[p]??p),referenceSample:n.referenceSample||r?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let d=e.showGenes?e.geneTrack:void 0,c=d?(0,Yi.getSession)(e).tracks.find(p=>p.trackId===d.trackId):void 0,m=c?(0,Ut.expandTabixShorthand)((0,Ut.readConfObject)(c,"adapter"),"gffGzLocation"):void 0,g=m?.type==="Gff3TabixAdapter"?{file:Pe(m.gffGzLocation),index:Pe(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:g?.file&&g.index?g:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,quality:e.layoutQuality,bubbleSpread:e.bubbleSpread,walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges||void 0}))},get figureUnavailable(){return e.layoutResult?e.drawsNodes||e.walkRowBars?void 0:`${_(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 ${_(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?mi(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.colorDomain,fitToDrawing:e.popStack.length>0,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?hi(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-$}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?Mo(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?Ke(r,o):void 0;return t&&n&&a?Go(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&&No(o.yScale)?r.mismatches.filter(i=>Po(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?fi(r,o,t,n):null)??To(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));var qi=Ki.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=ct(n,t);Ua(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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-`).then(()=>{r.notify("Figure spec copied. 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 Wo({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:r=>{e.showInLinearView(r)},onShowSynteny:r=>{e.showSyntenyView(r)}}))(0,ps.pushLaunchViewMenuItem)(t,n);return t}}));function rn(){return us}var Jn=y(K(),1);function ms(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function ls(e){let t=(0,Jn.readConfObject)(e,"assemblyNames"),n=ms(t)?t.slice(1):[];return n.length>0?n:void 0}function on(e){let t=(0,Jn.readConfObject)(e,"assemblyNames");return ms(t)?t[0]:void 0}function an(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 Dc(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function Zn(){return X.types.compose("GraphGenomeView",gs.BaseViewModel,rn(),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,Qe)})).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,hs.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 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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,fs.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!V(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Vc=(0,ws.defineLaunchKeys)()({});function Qn(e){e.addViewType(()=>new ys.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Zn(),launchKeys:Vc,ReactComponent:(0,bs.lazy)(()=>import("./chunks/GraphGenomeView-TKK67NXR.js"))}))}var ks=y(K(),1),Ie=y(me(),1),er=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function _c(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"),...er.map(o=>r(n(o)))].filter(o=>o!==void 0)}function tr(e){e.addTrackType(()=>{let t=(0,ks.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ie.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ie.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ie.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of _c(e))n.addDisplayType(r);return n})}function nr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Vs=y(De(),1),_s=y(Ss(),1);var vs=y(K(),1),Gs=y(Ms(),1),rr=y(oe(),1);function Ls(){return(0,vs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:rr.types.enumeration("LayoutMode",yt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:rr.types.enumeration("ColorScheme",wt),defaultValue:"auto"},...(0,Gs.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Bs=y(De(),1);var ct=y(K(),1),Fs=y(me(),1),Os=y(Cr(),1),ar=y(ie(),1),$s=y(Ts(),1),F=y(oe(),1),Be=y(Ns(),1);var dt=y(ut(),1);var sn=y(ie(),1),Ee=y(oe(),1);function Cs(e){return e instanceof Error&&(e.name==="NodeLimitError"||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Is(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 or=class extends Error{constructor(){super("this window is too large to cut, and there is no overview to draw instead: either the haplotype index has none (rebuild it with gbz-haplotype-index 0.3 or later) or the reference has no path by this name. Zoom in to see the graph");this.name="NoOverviewError"}};function Es(){return Ee.types.model({overviewRowsChoice:Ee.types.maybe(Ee.types.boolean)}).volatile(()=>({overview:void 0,overviewRegion:void 0,overviewBpPerPx:0,overviewLoading:!1,overviewError:void 0,overviewPainted:void 0,overviewController:void 0,dense:void 0})).views(e=>({get overviewAllRows(){return e.overviewRowsChoice??!0},get overviewCounts(){return e.overview&&e.overview.bin<=jo?Xo(e.overview):void 0},overviewHolds(t){return e.overview!==void 0&&e.overviewError===void 0&&Ct(e.overviewRegion,t)&&t.bpPerPx>=e.overviewBpPerPx/2&&t.bpPerPx<=e.overviewBpPerPx*2}})).actions(e=>({setOverviewAllRows(t){e.overviewRowsChoice=t},beforeDestroy(){e.overviewController?.abort()},setOverviewPainted(t){e.overviewPainted=t},setDense(t){e.dense=t},forgetOverview(){e.overviewController?.abort(),e.overview=void 0,e.overviewRegion=void 0,e.overviewLoading=!1},fetchOverview:(0,Ee.flow)(function*(t,n,r){e.overviewController?.abort();let o=new AbortController;e.overviewController=o,e.overviewLoading=!0,e.overviewError=void 0;let a=Nt(n,1/0);try{let i=yield(0,sn.getSession)(e).rpcManager.call((0,sn.getRpcSessionId)(e),"GetHaplotypeOverview",{adapterConfig:t,region:a,bpPerPx:n.bpPerPx*2,haplotypes:r,signal:o.signal});o.signal.aborted||(e.overview=i,e.overviewRegion=a,e.overviewBpPerPx=n.bpPerPx,i||(e.overviewError=new or))}catch(i){o.signal.aborted||(console.error("[HaplotypeOverview]",i),e.overviewError=i instanceof Error?i:new Error(String(i)))}finally{e.overviewController===o&&(e.overviewLoading=!1)}})}))}var Wc=(0,Bs.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-RKZ5XIKY.js"));function Ds(e){return F.types.compose("LinearGraphDisplay",Fs.BaseDisplay,(0,$s.default)(),rn(),Es(),F.types.model({type:F.types.literal("LinearGraphDisplay"),configuration:(0,ct.ConfigurationReference)(e),pane:F.types.maybe(F.types.frozen()),cutRegion:F.types.maybe(F.types.frozen()),coarseCut:F.types.optional(F.types.boolean,!1),maxRegionBp:F.types.optional(F.types.number,Qe),subgraphContext:F.types.optional(F.types.number,1),subgraphHaplotypes:F.types.maybe(F.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,ct.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,ct.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??ls(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${be(n.end-n.start)}, max ${be(t.settledCapBp)})`:""},get overviewCapable(){return t.adapterConfig.type==="GbzBaseSyntenyAdapter"},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get showsOverview(){let n=t.settledWindow;return t.overviewCapable&&n!==void 0&&(t.regionTooLarge||Is(t.dense,n))}})).views(t=>({get overviewPhase(){return(0,Be.computeDisplayStatusPhase)({regionTooLarge:!1,error:t.overviewError},()=>(0,Be.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.overviewLoading||!t.overview,fetchCanceled:!1,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.overview!==void 0&&t.overviewPainted===t.overview},()=>!0,()=>t.host?.effectiveBodyMounted??!0))},get displayPhase(){return t.showsOverview?this.overviewPhase:(0,Be.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,Be.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.forgetOverview()},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.settledWindow;if(n&&t.showsOverview)return t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes);let r=t.cutRegion;if(!r)return;let o=an(on(t.parentTrack.configuration),r.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let a=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,r,{hops:a?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:a?"coarse":void 0,...V(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Nt(n,t.capFor(r),V(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){if(t.settledWindow=n,t.showsOverview)return t.overviewHolds(n)||t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes),!1;let r=V(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Ct(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,F.isAlive)(t)&&t.overviewCapable&&Cs(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=V(t.chosenLayoutMode);t.setLayoutMode(n);let o=V(n),a=t.host?Pt(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,dt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,F.addDisposer)(t,(0,dt.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,dt.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let 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0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,I.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,nr.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Fs.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Nt,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),{label:"Settings",icon:Ho,onClick:()=>{(0,nr.getSession)(t).queueDialog(r=>[_c,{model:t,open:!0,onClose:r}])}},...n]}}))}function rr(e){e.addDisplayType(()=>{let t=Ts();return Object.assign(new _s.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Ds(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Vs.lazy)(()=>import("./chunks/LinearGraphDisplay-GKVG72J4.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Hs=w(Pt(),1);var or=w(U(),1),Ws=w(re(),1);function ar(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Wc=(0,or.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,or.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Ws.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:ar}),Os=Wc;function ir(e){e.addAdapterType(()=>new Hs.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:ar,configSchema:Os,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CZYQROL2.js").then(t=>t.default)}))}var Us=w(Pt(),1);var rn=w(U(),1),zs=w(re(),1);function js(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Xs(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:js(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:js(`${t}.links.bed.gz`,n,r)}:e}function sr(e){let{coarse:t,baseUri:n}=e;return Xs(typeof t=="object"&&t!==null?{...e,coarse:Xs({baseUri:n,...t})}:e)}var nn=(e,t)=>(0,rn.ConfigurationSchema)(e,{indexType:{model:zs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Oc=(0,rn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:nn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:nn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Hc=(0,rn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:nn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:nn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Oc},{explicitlyTyped:!0,preProcessSnapshot:sr}),Ys=Hc;function dr(e){e.addAdapterType(()=>new Us.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:sr,configSchema:Ys,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-LQGQXCVO.js").then(t=>t.default)}))}var jc=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Xc(e){return Tr(e).toLowerCase().endsWith(".gbz.db")}function zc(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 Yc(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Xc(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Ar(e))return Nr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function cr(e){e.addToExtensionPoint("Core-preProcessTrackConfig",zc),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>Yc(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>jc.has(n)?"GraphTrack":t(n,r))}var Zs=w(oe(),1),Qs=w(hd(),1),pr=w(gd(),1),ed=w(bd(),1);function Ks(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 Uc(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 Kc(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 Js(e,t,n){let r=[],o=Qe(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 Kc(i)){let d=Ks(s.hoverHighlight);d&&qs(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(Q(i)&&i.type==="GraphGenomeView"&&Uc(i,t,a)){let s=Ks(i.hoverHighlight);s&&qs(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ie=w(Be(),1),qc=(0,ed.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Qs.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),Jc=(0,pr.observer)(function({model:t,region:n}){let{classes:r}=qc(),o=t.getHighlightCoords(n);return o?(0,Ie.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Zc=(0,pr.observer)(function({model:t}){let{views:n}=(0,Zs.getSession)(t);return(0,Ie.jsx)(Ie.Fragment,{children:Js([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Ie.jsx)(Jc,{model:t,region:o},`graph-hover-${r}`))})}),td=Zc;var nd=w(Be(),1),Qc="LinearGenomeView-TracksContainerComponent";function ur(e){e.contributeToExtensionPoint(Qc,({model:t})=>(0,nd.jsx)(td,{model:t},"graphgenomeview-hover-highlight"))}var rd=w(le(),1);function ep(e){return e.views(t=>({get adapterConfig(){return ge(t,t.parentTrack.configuration)}}))}function mr(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rd.DisplayType&&Zn.includes(t.name)&&t.extendStateModel(ep),t))}var od="GraphGenomeView";var ad="5.2.0";var lr=class extends id.default{constructor(){super(...arguments);this.name=od;this.version=ad}install(n){Jn(n),rr(n),Qn(n),er(n),ur(n),dr(n),ir(n),yn(n),kn(n),cr(n),mr(n),n.addRpcMethod(()=>new Oe(n)),n.addRpcMethod(()=>new We(n)),n.addRpcMethod(()=>new _e(n))}configure(n){try{(0,sd.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Nt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{lr as default};
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