jbrowse-plugin-graphgenomeviewer 7.3.1 → 7.3.2

package/dist/chunks/chunk-JCAZTNYG.js

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package/dist/chunks/chunk-N74HGPAW.js

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e.drawnGraph?Z(e.drawnGraph):void 0},get nodeInk(){return ze(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?xe(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?Fa(n,t,t.unit):me(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[a,...r]=_o([o.reference,...o.rows],t?.calls);return{...o,reference:a,rows:r}},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&&vn(t)?t:void 0},get walkRowGroupFields(){return io(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=fo(t,n),a=(e.graph?.paths??[]).map(r=>X(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:uo(a.map(o)),unvalued:a.some(r=>o(r)==="")}},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;return t&&Me(t.rows,e.walkRowSamples)},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 drawsNodes(){return F(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ge(e.positionsVersion);let t=e.layoutResult?.nodePositions;return 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t!==null?Tr(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 Er=Gr.views(e=>({get host(){let t=e.containingView;return sr(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?tr(t,{maxGap:n.length>0?kt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Y(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,s])=>[s,r])),a=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>a(o.get(r))??a(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(it.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let a=ct(o,"");return 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n)a(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:s},i)=>{(n.has(r)||n.has(s))&&(a(e.edgeCurves,e.edgeCurveRuns.get(i)),a(e.arrows,e.arrowRuns.get(i)))})}function Ka(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function Bg(e,t,n,o){return!(e.referenceAxis||t.referenceAxis||e.pixelRows||t.pixelRows||t.tubeMap||o||n>Ha)}function Og(){return typeof requestAnimationFrame<"u"&&!("matchMedia"in window&&window.matchMedia("(prefers-reduced-motion: reduce)").matches)}function _g(e,t,n){let o={frame:0,finish:()=>{e(1)}},a=0,r=performance.now(),s=()=>{if(!t()){n();return}let i=performance.now();a+=Math.min(i-r,Xa),r=i;let c=Math.min(1,a/Da);e(Ka(c)),c<1?o.frame=requestAnimationFrame(s):n()};return o.frame=requestAnimationFrame(s),o}function $g(e,t,n,o){for(let[a,r]of Object.entries(e)){let s=t[a],i=n[a];!s||!i||r.forEach((c,d)=>{c.x=o===1?i[d].x:s[d].x+(i[d].x-s[d].x)*o,c.y=o===1?i[d].y:s[d].y+(i[d].y-s[d].y)*o})}}var Ja=8,qa=19,_r=Pe+qa,Za=48;function Qa(e,t,n){if(!(!e||!t))return Je(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var iw=Cr.views(e=>({get paneCeiling(){return Math.max(ot,e.paneHeight??zn)},get fitRoom(){return e.host?this.canvasHeight:this.paneCeiling},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=this.fitRoom,o=(e.walkRowGroups?.sections.length??0)*so;return qe(t.rows.length+1,n-this.fitPadTopBase-C-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?mo(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return Qa(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=he(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,a)=>({...o,y:t.rowY(a)})):n},get visibleRowLabels(){return this.drawnRowLabels.flatMap(({label:t,y:n})=>{let o=e.toScreen({x:0,y:n}).y;return o>=0&&o<=this.canvasHeight?[{label:t,y:n,top:o}]:[]})},get fitPadLeft(){return Math.max(C,...this.drawnRowLabels.map(t=>Tn(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ue(n,this.walkRowPitch):void 0;return t?Te(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,a=o?t.reference:t.rows.find(r=>r.name===n);return a?{label:a.label,readout:Wn(a,o?void 0:t.reference,t.unit,a.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,a=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!a||!r)return;let s=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][s],c=r.rowY(s)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=a.barPx/2+2&&d>=0&&d<=i.bp?s:void 0},get fitPadTopBase(){let t=Po(e.tubeMapGenes);return C+Math.max(0,t-1)*No+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let a=this.fitPadTopBase,r=this.fitRoom,s=l=>(e.paneWidth-this.fitPadLeft-l)/t.w,i=l=>e.pixelRows?t.h+l+C<=r?1/0:0:(r-l-C)/t.h,c=Math.min(s(n+2*ee),i(a));return Math.min(s(C),i(a+o+ee))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ee:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(C,e.legendSize.width+2*ee):C},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(Un/o,(this.paneCeiling-this.fitPadTop-C)/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?tt(t.map(a=>a.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?Qe({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-_r)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ee+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-Za?t+2*ee:Ja},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(ot,o.total+_r);let a=Math.max(ot,e.legendSize.height+2*ee+e.referenceStripZonePx),r=this.fitPads,s=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(a,t.h+s));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(a,t.h*Math.max(i/t.w,this.minFitScale)+s)):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:U,top:U,right:U,bottom:U}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:C}},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,a=this.fitPads;return t?Ae(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:a.left,padTop:a.top,padRight:a.right,padBottom:a.bottom}):void 0}})).views(e=>({viewportToBuild(){return Xn(Qn(e),qn)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,Jn]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=$o();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:Yn)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:a,layoutResult:r,deletionDrawing:s}=e;if(!o||!a||!r||!s)return;Ge(e.viewportDirty,e.positionsVersion);let i=Lt(()=>e.viewportToBuild()),c=Ue({..._e(r,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:Lt(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Or(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return xo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Mo(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,a=t&&`${t.refName}:${t.start}-${t.end}`,r=le(e.sourceGfaLocation),s=n?.type==="GbzBaseSyntenyAdapter"?le(n.gbzDbLocation):void 0,i=r?{gfa:r,region:a}:s&&t&&a?{gbz:{db:s,index:le(n.haplotypeIndexLocation),region:a,haplotypes:e.cutHaplotypes?.map(p=>o?.[p]??p),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!i)return;let c=e.showGenes?e.geneTrack:void 0,d=c?e.sessionTrack(c.trackId):void 0,l=d?Rn(_(d,"adapter"),"gffGzLocation"):void 0,m=l?.type==="Gff3TabixAdapter"?{file:le(l.gffGzLocation),index:le(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...i,genes:m?.file&&m.index?m:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...Qt({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.statedColorDomain}),walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${F(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 ${F(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?nn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps},spec:e.drawsNodes?this.figureSpec():void 0}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var fn=$(W("path",{d:"M3 16h5v-2H3zm6.5 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