jbrowse-plugin-graphgenomeviewer 7.4.4 → 7.5.0

package/dist/chunks/chunk-DAPI7M4M.js

@@ -0,0 +1,4 @@
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e.domainMax=="number"?{start:e.domainMin,end:e.domainMax}:void 0}function lf(e,t){return e==="grey"||e==="uniform"?e:e==="random"?{field:"id",scale:"categorical"}:e==="rainbow"?{field:"id",scheme:"rainbow"}:e==="reference-position"&&t?{field:"position",domainMin:t.start,domainMax:t.end}:_r[e]?{field:_r[e]}:{}}var Hr=6;function kt(e){return typeof e=="number"?{width:"uniform",px:e,links:"uniform"}:Y(e)?{width:e.field==="depth"?"depth":"uniform",px:typeof e.value=="number"?e.value:Hr,links:e.links==="walks"?"walks":"uniform"}:{width:"depth",px:Hr,links:"uniform"}}function hf({width:e,px:t,links:n}){return e==="uniform"&&n==="uniform"?t:{...e==="depth"?{field:"depth"}:{},value:t,...n==="walks"?{links:n}:{}}}function Fr(e,t,n,o){let r=En(e,t,{visits:o});return r?Tt(r,n):void 0}function Dr(e){try{return e()}catch{return}}function Vr(e){let t=new Map;for(let n of e.nodes)t.set(n.id,n);return t}function Xr(e,t,n){return t&&n?Et({nodeId:e,nodeById:t,neighbors:n}):void 0}var 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t=e.drawnGraph;return t?Ee(t,this.rampDomain):void 0},get walkRamp(){return e.walkLayers.some(t=>t.color?.field==="reference")?this.drawnReferenceRamp:void 0},get modeDrawsNodes(){return z(e.chosenLayoutMode).drawsNodes},get liftedWalkLayers(){return e.walkLayers.length>0||!this.modeDrawsNodes?e.walkLayers:e.hoveredRowWalks.map(t=>({walk:t}))},get walkLift(){let{graph:t}=e,n=this.liftedWalkLayers;return t&&!e.walkCut&&n.length>0&&!e.layoutResult?.tubeMap?He(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facetSetting.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?Fe(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!oo.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Ye(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(Qn))},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":De(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?bt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>bt(Xe(t,de(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(de(t)),r=new Set(n.nodes.filter(a=>o.has(a.name)).map(a=>a.id)),s=new Set;return n.edges.forEach((a,i)=>{r.has(a.from)&&r.has(a.to)&&s.add(i)}),{walks:[],nodeIds:r,edgeIndexes:s,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>ot(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(s=>o.nodeIds.has(s)):!!r&&!this.bubbleIsOpen(t)&&!n.every(s=>r.nodeIds.has(s))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(rt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(rt(o))&&n.add(rt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${$n(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?er(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?X(t,"trackId"):void 0},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:X(n,"name"),adapterType:X(n,"adapter").type,assemblies:Qt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Zt(U(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>dt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>jo.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return zo(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return pt(e.geneTrackChoices,e.geneTrackId)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?Lt(e.graph):void 0},get cutWalkRows(){let t=e.walkCut,n=t?.walkRowRuns,o=this.rowVisitsNeeded;return t&&n&&o&&e.graphRegion?Fr(t,e.graphRegion,void 0,!0):n?Tt(n):e.graph?he(e.graph,e.graphRegion,void 0,{visits:o}):void 0},get rowVisitsNeeded(){return e.chosenLayoutMode==="walkrows"&&(e.walkRibbons||e.layerSet.has("walkBlocks")||e.walkRowOrder==="shared")},assemblySpellings(t){let{assemblyManager:n}=U(e),o=n.has(t)?n.get(t):void 0,r=e.sourceAdapter?.assemblyNameToPanSN??{},s=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...s,...s.flatMap(a=>r[a]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t=e.containingView;if(!t)return;let n=Yo(t,e.geneTrack?.trackId);return n.length?new Cr({filters:n,jexl:Mn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Uo(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,r=e.drawsLoadedReference||n!==void 0&&Pt(t,[n])!==void 0;return 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t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=No(t,n),r=(e.graph?.paths??[]).map(s=>W(s.name).name).filter(s=>s!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Mo(r.map(o)),unvalued:r.some(s=>o(s)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&Pe(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return wn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?xo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowRibbons(){let t=this.walkRowBars;if(!e.walkRibbons||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return bn(n,be(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return yn(n,be(n))},get drawsNodes(){return z(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ie(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?$e(e.graph,n,t):[]},get bubbleHalos(){Ie(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:dn(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return Ze(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Le(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return e.drawsNodes||!!e.layoutResult?.tubeMap},get referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!B(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?kn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!ze(n.length)||n.some(r=>r.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],r=this.tubeColorKind,s=e.tubeMapColoring;return r==="value"&&s?Lo(o,t.referencePath,s.valueOf,s.palette):r==="tinted"?Xt(o,t.referencePath,vo):r==="role"?Xt(o,t.referencePath):n},fadeUnhovered(t,n,o){let r=new Set(e.hoveredRowWalks);return r.size>0?t.map((s,a)=>{let i=n[a]?.name??"";return r.has(i)||o!==void 0&&W(i).name===o?s:et}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return Xr(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&Vr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&Q(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&ze(t.length)&&!t.some(o=>o.members)?Ne(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?Xr(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var zr=jr.views(e=>({get host(){let t=e.containingView;return qo(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?q(t):[];return t?ur(t,{maxGap:n.length>0?vt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=U(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([s,a])=>[a,s])),r=s=>s!==void 0&&t.has(s)?t.get(s)?.name??s:void 0;return s=>r(o.get(s))??r(s)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(dt.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let r=pt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return hr(wr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Ce({views:[...U(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?Jt(n):void 0,r=o?me(e.assemblyResolver,o):void 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tn({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:Pe(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return _e(t,{width:e.paneWidth})},cutsWholeWalksIn(t,n=e.walkStrip){let o=z(t);return e.sourceAdapter?.type==="GbzBaseSyntenyAdapter"&&nn(o,{walkStrip:n&&o.drawsNodes,host:!!e.host})},get cutsWholeWalks(){return this.cutsWholeWalksIn(e.chosenLayoutMode)},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?on(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:me(e.assemblyResolver,o),span:{refName:n.contig,...st(n,t.bp)}}},get walkStripLocator(){let 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t&&t.h>0&&o&&!n.referenceAxis?Math.min(no/o,(this.paneCeiling-this.fitPadTop-O)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?qe(t.map(r=>r.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?Ke({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-qr)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=te+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-ga?t+2*te:ha},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(nt,o.total+qr);let r=Math.max(nt,e.legendSize.height+2*te+e.referenceStripZonePx),s=this.fitPads,a=s.top+s.bottom;if(e.pixelRows)return Math.min(n,Math.max(r,t.h+a));let i=e.paneWidth-s.left-s.right;return t.w>0&&i>0?Math.min(n,Math.max(r,t.h*Math.max(i/t.w,this.minFitScale)+a)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:K,top:K,right:K,bottom:K}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:O}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,r=this.fitPads;return t?Te(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:r.left,padTop:r.top,padRight:r.right,padBottom:r.bottom}):void 0}})).views(e=>({viewportToBuild(){return Dn(co(e),so)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new 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