jbrowse-plugin-graphgenomeviewer 7.5.0 → 7.7.0

package/dist/chunks/chunk-AK3UZI6J.js

@@ -0,0 +1,4 @@
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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(Jn))},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":$e(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(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(De(t,le(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(le(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=>nt(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(ot));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(ot(o))&&n.add(ot(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?Zo(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?V(t,"trackId"):void 0},get sessionTracks(){let t=z(e);return t.tracks.map(n=>({trackId:n.trackId,name:V(n,"name"),adapterType:V(n,"adapter").type,assemblies:Kt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Ut(z(e),t.assemblyName);return 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e.layoutResult?.tubeMap&&t?gn(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&&(!je(n.length)||n.some(r=>r.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],r=this.tubeColorKind,a=e.tubeMapColoring;return r==="value"&&a?So(o,t.referencePath,a.valueOf,a.palette):r==="tinted"?Ht(o,t.referencePath,Ro):r==="role"?Ht(o,t.referencePath):n},fadeUnhovered(t,n,o){let r=new Set(e.hoveredRowWalks);return r.size>0?t.map((a,s)=>{let i=n[s]?.name??"";return r.has(i)||o!==void 0&&pe(i).name===o?a:Qe}):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 Wr(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 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