jbrowse-plugin-graphgenomeviewer 8.3.8 → 8.3.9

package/dist/chunks/chunk-CFW2JQMT.js

@@ -0,0 +1,4 @@
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t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Xe(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(ao))},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":Ce(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?yt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>yt(We(t,pe(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(pe(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 ${jn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?dr(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:$n(n,t),adapterType:Ye(n).type,assemblies:Qt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Zt(U(e),t.assemblyName);return 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t=e.sourceAdapter?.samplesTsvLocation;return t&&Bn(t)?t:void 0},get walkRowGroupFields(){return Lo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Bo(t,n),r=(e.graph?.paths??[]).map(a=>de(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Eo(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 bn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Po(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 walkRowList(){let t=this.walkRowBars;return t?[t.reference,...t.rows]:[]},get walkRowRibbons(){let t=this.walkRowGroups?.sections??[];return e.walkRibbons&&e.rowVisitsNeeded&&this.walkRowBars?yn(this.walkRowList).filter(({row:n})=>Vt(t,n)===Vt(t,n+1)):void 0},get sharedBlocks(){return e.layerSet.has("walkBlocks")&&e.rowVisitsNeeded&&this.walkRowBars?kn(this.walkRowList):void 0},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Pe(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ie(e.graph,n,t):[]},get bubbleHalos(){Pe(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 qe(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 referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!A(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?Rn(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&&(!Ve(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?Io(o,t.referencePath,a.valueOf,a.palette):r==="tinted"?Xt(o,t.referencePath,Go):r==="role"?Xt(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&&de(i).name===o?a:Qe}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return 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n&&e.graph&&e.chosenHover!=="off"?kr(e.graph,n,e.assemblyResolver,e.graphRegion?.assemblyName):[]}}));var ea=Qr.views(e=>({get walkStripShown(){return 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:ve(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ee(t,{width:e.paneWidth})},cutsWholeWalksIn(t,n=e.walkStrip){let o=Y(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 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