jbrowse-plugin-graphgenomeviewer 8.1.0 → 8.2.0

package/dist/chunks/{chunk-5EWKB2JM.js → chunk-MCBYBZZJ.js}

@@ -1,4 +1,4 @@
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package/dist/chunks/{chunk-IL5HOUFN.js → chunk-NOXHIOIM.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-OG7MODXE.js → chunk-OLZZDBQJ.js}

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e.get(i)??[])n.has(d)&&!t.has(d)&&(t.set(d,{at:c.at,side:1,hops:c.hops+1}),o.push(d))}let a=new Set(o.slice(r)),s=new Set;for(let i of a){if(s.has(i))continue;let{at:c}=t.get(i),d=[i];s.add(i);let m=!0;for(let l of d){let{hops:p}=t.get(l),u=!0,h=!1;for(let f of e.get(l)??[]){let g=t.get(f);g&&(g.at===c&&a.has(f)?(u&&=g.hops<=p,s.has(f)||(s.add(f),d.push(f))):g.at!==c&&(h||=g.at<c,m&&=g.at<c))}m&&=!u||h}if(m)for(let l of d){let p=t.get(l);t.set(l,{...p,side:-1,hops:-p.hops})}}}function ba(e){let t=e.nodes.filter(T).sort((o,r)=>ne(o.stable.start,r.stable.start)||ne(o.name,r.name)),n=new Map;return ga(e,t).forEach((o,r)=>{n.set(o,{at:r,side:0,hops:0})}),wa(Q(e),n,new Set(e.nodes.map(o=>o.id))),n}function ya(e){let t=new Map(e.nodes.map(l=>[l.id,l])),n=Xt(e),o=new Map(n.map((l,p)=>[l,p])),r=l=>T(t.get(l)),a=new Map(n.map(l=>[l,[]])),s=new Map(n.map(l=>[l,[]])),i=(l,p)=>{a.get(p).push(l),s.get(l).push(p)};for(let l of 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e.get(i)??[])n.has(d)&&!t.has(d)&&(t.set(d,{at:c.at,side:1,hops:c.hops+1}),o.push(d))}let a=new Set(o.slice(r)),s=new Set;for(let i of a){if(s.has(i))continue;let{at:c}=t.get(i),d=[i];s.add(i);let m=!0;for(let l of d){let{hops:p}=t.get(l),u=!0,h=!1;for(let f of e.get(l)??[]){let g=t.get(f);g&&(g.at===c&&a.has(f)?(u&&=g.hops<=p,s.has(f)||(s.add(f),d.push(f))):g.at!==c&&(h||=g.at<c,m&&=g.at<c))}m&&=!u||h}if(m)for(let l of d){let p=t.get(l);t.set(l,{...p,side:-1,hops:-p.hops})}}}function ba(e){let t=e.nodes.filter(T).sort((o,r)=>ne(o.stable.start,r.stable.start)||ne(o.name,r.name)),n=new Map;return ga(e,t).forEach((o,r)=>{n.set(o,{at:r,side:0,hops:0})}),wa(Q(e),n,new Set(e.nodes.map(o=>o.id))),n}function ya(e){let t=new Map(e.nodes.map(l=>[l.id,l])),n=Xt(e),o=new Map(n.map((l,p)=>[l,p])),r=l=>T(t.get(l)),a=new Map(n.map(l=>[l,[]])),s=new Map(n.map(l=>[l,[]])),i=(l,p)=>{a.get(p).push(l),s.get(l).push(p)};for(let l of 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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(He(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(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>tt(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(nt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(nt(o))&&n.add(nt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Fn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?or(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=Y(e);return t.tracks.map(n=>({trackId:n.trackId,name:Cn(n,t),adapterType:je(n).type,assemblies:Jt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Kt(Y(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>pt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Uo.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Ko(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return lt(e.geneTrackChoices,e.geneTrackId)},get walkRowAnnotation(){return mt(this.geneTrack)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?Nn(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?Pt(n):e.graph?ue(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}=Y(e),o=n.has(t)?n.get(t):void 0,r=e.sourceAdapter?.assemblyNameToPanSN??{},a=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...a,...a.flatMap(s=>r[s]??[])]}},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=Jo(t,e.geneTrack?.trackId);return n.length?new Br({filters:n,jexl:xn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?qo(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&&Pn(t,[n])!==void 0;return t&&o&&r?An(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?Q(e.drawnGraph):void 0},get nodeInk(){return qe(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get depthRange(){let t=e.graph?.nodes;if(!t?.length)return;let n=1/0,o=-1/0;for(let{depth:r}of t)n=Math.min(n,r),o=Math.max(o,r);return{min:n,max:o,mean:qn(e.graph)}},get busiestLink(){return e.graph?Zn(e.graph):0},get allDeletions(){return e.graph&&this.drawsNodes?Fe(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=e.rowVisitsNeeded,r=t?n?Fr(n,t,t.unit,o):ue(e.graph,t,t.unit,{visits:o}):e.cutWalkRows;if(!r)return;let[a,...s]=Zo([r.reference,...r.rows],t?.calls);return{...r,reference:a,rows:s}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&Tn(t)?t:void 0},get walkRowGroupFields(){return xo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Ao(t,n),r=(e.graph?.paths??[]).map(a=>ce(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Lo(r.map(o)),unvalued:r.some(a=>o(a)==="")}},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,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&ve(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return hn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?vo(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 fn(n,we(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return gn(n,we(n))},get drawsNodes(){return j(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ce(e.graph,n,t):[]},get bubbleHalos(){Ae(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?[]:an(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 Je(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?De(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 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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&&Ve(t.length)&&!t.some(o=>o.members)?Se(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 Yr=jr.views(e=>({get host(){let t=e.containingView;return er(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?J(t):[];return t?gr(t,{maxGap:n.length>0?vt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Y(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([a,s])=>[s,a])),r=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>r(o.get(a))??r(a)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(pt.has(n.adapterType)&&mt(n)===e.walkRowAnnotation)for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let r=lt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return wr(kr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get 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package/dist/chunks/{chunk-PKMASUMB.js → chunk-PTOKTIQG.js}

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