npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.2.0 → 6.3.0 - Mend

jbrowse-plugin-graphgenomeviewer 6.2.0 → 6.3.0

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package/dist/jbrowse-plugin-graphgenomeviewer.esm.js CHANGED Viewed

@@ -1,9 +1,9 @@
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t&&n&&o&&this.walkRowGroupFields.includes(o.field)?$r(ve(t.rows,e.walkRowSamples),n,o):void 0},get walkRowBars(){let t=this.cohortWalkRows;return t?{...t,rows:this.walkRowGroups?.rows??ve(t.rows,e.walkRowSamples)}:void 0},get drawsNodes(){return!e.layoutResult?.tubeMap&&!this.walkRowBars},get genePins(){le(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?it(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){le(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:bo(e.graph,e.bubbles,t,n=>e.walkLabel(n),e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Ge(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return ke(e.scale,e.pixelRows).scaleX},get scaleY(){return ke(e.scale,e.pixelRows).scaleY},get axisScale(){return ke(e.scale,e.pixelRows)}})).views(e=>({get deletionDrawing(){return e.graph?_e(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 referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,o=n?.tubeMap?n.nodePositions:void 0,r=!1,a=!1;if(t&&e.drawnGraph)for(let i of e.drawnGraph.nodes)o&&!o[i.id]||(t.midpoints.has(i.id)?i.stable&&i.stable.rank>0&&(r=!0):a=!0);return{offReference:r,unplaced:a}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?yo(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>hr(i,t.length)):t,o=new Set(e.hoveredRowWalks),r=e.drawnGraph?.paths;return n&&r&&o.size>0?n.map((a,i)=>o.has(r[i]?.name??"")?a:Lr):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:o}=e;return n&&o?be({nodeId:t,nodeById:n,neighbors:o}):void 0}})).views(e=>({get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&Mn(t.length)?je(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?e.nodeSpan(t):n?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return t&&n?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var To=y(q(),1);function Q(e){return typeof e=="object"&&e!==null}function Wd(e){return Q(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function lt(e){return e.flatMap(t=>Q(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function gt({views:e,connectedViewId:t,assemblyName:n}){let o=lt(e).filter(a=>Wd(a)).filter(a=>a.assemblyNames.includes(n));return o.find(a=>a.id===t)??(o.length===1?o[0]:void 0)}function ht(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function ss(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var Hd=1e3;function vo(e,t=Hd){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function cs(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function ds({session:e,location:t,assembly:n,connectedViewId:o,tracks:r=[]}){let a=gt({views:e.views,connectedViewId:o,assemblyName:n}),i;return a?(ss(e,`Could not show ${n} ${Ke(t)}`,Promise.resolve(a.navToLocString(Ot(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${Ke(t)}`,init:{assembly:n,loc:Ot(t),tracks:r}}).id,i}function ps({session:e,location:t,assembly:n,connectedViewId:o}){let r=gt({views:e.views,connectedViewId:o,assemblyName:n});return r&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n}),r!==void 0}function is(e,t){if(t===void 0)return[];let n=e.tracks.find(r=>(0,To.readConfObject)(r,"trackId")===t),o=n?(0,To.readConfObject)(n,"assemblyNames"):[];return Array.isArray(o)?o.filter(r=>typeof r=="string").map(r=>ht(e,r)):[]}function us({session:e,contributors:t,trackId:n,graphTrackId:o}){let r=is(e,o),a=is(e,n),i=t.filter(d=>a.includes(d.sample)),s=i.length>=2?i:t,c={init:{views:s.map(d=>({assembly:d.sample,loc:Ot(d),...o!==void 0&&r.includes(d.sample)?{tracks:[o]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?ss(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c)):e.addView("LinearSyntenyView",c)}var ms=as.views(e=>({get contributingAssemblies(){let t=e.graph,n=t?tr(t):[];return t?va(t,{maxGap:n.length>0?rr(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,Me.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([a,i])=>[i,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(0,Me.getSession)(e).tracks){let o=(0,nn.readConfObject)(n,"adapter").type;if(!pt.has(o))continue;let r={trackId:n.trackId,name:(0,nn.readConfObject)(n,"name"),adapterType:o};for(let a of(0,nn.readConfObject)(n,"assemblyNames")){let i=ht((0,Me.getSession)(e),a);t.set(i,[...t.get(i)??[],r])}}return new Map([...t].flatMap(([n,o])=>{let r=Qt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return Ga(cs(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&gt({views:[...(0,Me.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?Ye(n):void 0,r=o?Ue(e.assemblyResolver,o):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,c=a&&i&&s?be({nodeId:t,nodeById:i,neighbors:s}):void 0,d=a&&c?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...c}:void 0;return{own:o&&r?{location:vo(o),assembly:r}:void 0,reference:a&&d?{location:vo(d),assembly:a.assemblyName}:void 0,highlight:a&&d?{location:d,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,Me.getContainingView)(e)}catch{return}return zi(t)?t:void 0}}));var ls=ms.views(e=>({get walkStripShown(){return Ur({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,popped:e.popStack.length>0,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 $t(t,{width:e.paneWidth})},get cutsWholeWalks(){return Kr(H(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?qr(e.graph,[t.reference,...t.rows],o):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Vt(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,r=0;for(let a of t.rows){if(!a.axis){r++;continue}let i=Ue(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){o++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...Pn(a.axis,a.bp)}})}return{reads:n.slice(0,no),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-no)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let r=o.haplotype===void 0?void 0:`${o.sample}#${o.haplotype}`,a=t===0?e.graphRegion?.assemblyName:Ue(e.assemblyResolver,{sample:o.sample,haplotype:r});return{label:o.label,assembly:a,location:{sample:o.sample,haplotype:r,refName:o.axis.contig,...Pn(o.axis,o.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?zr([t.reference,...t.rows],n):void 0}}));var gs=ls.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&H(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 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referenceStripBlocks(){let{graph:t}=e;return e.showReferenceStrip&&e.referenceStripApplies&&t?Ra(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?dt(t,n):void 0}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.referenceStripFrame!==void 0},get referenceStripOverhangs(){let t=e.referenceStripFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:o}=xa(e.referenceStripBlocks,t,e.paneWidth);return n>0||o>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=a=>({x:a.x*e.scaleX+e.translateX,y:a.y*e.scaleY+e.translateY}),n=e.hoveredNode===null?e.hoveredBubble:null;if(n){let a=e.bubbleHalos.find(i=>Or(i.bubble,n));return{start:n.start,end:n.end,anchor:a?t(a.labelAt):void 0}}let o=e.hoveredNode??e.selectedNode,r=o===null?void 0:e.nodeSpan(o);return r&&o!==null?{...r,anchor:Vt(e.nodePositions?.[o],t)}:void 0},referenceStripNodeAt(t,n){let o=e.referenceStripFrame;return e.referenceStripShown&&o?La(e.referenceStripBlocks,o,t,n):void 0},get paperCss(){return wi(e.darkMode?Ut:Yt)},get referenceStripZonePx(){return e.referenceStripShown?Sa:0}}));function jd(e,t,n){if(!(!e||!t))return Xr(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var fs=gs.views(e=>({get paneCeiling(){return Math.max(Xt,e.paneHeight??bi)},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=e.host?this.canvasHeight:this.paneCeiling,o=(e.walkRowGroups?.sections.length??0)*Er;return Yr(t.rows.length+1,n-this.fitPadTopBase-F-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?Vr(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return jd(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=Xe(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,r)=>({...o,y:t.rowY(r)})):n},get fitPadLeft(){return Math.max(F,...this.drawnRowLabels.map(t=>gr(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ze(n,this.walkRowPitch):void 0;return t?tt(t,{region:e.popStack.length===0?e.graphRegion:void 0,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,r=o?t.reference:t.rows.find(a=>a.name===n);return r?{label:r.label,readout:jr(r,o?void 0:t.reference,t.unit,r.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,r=this.walkRowPitch,a=this.walkRowPlacement;if(!o||!r||!a)return;let i=a.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),s=[o.reference,...o.rows][i],c=a.rowY(i)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return s&&Math.abs(n-c)<=r.barPx/2+2&&d>=0&&d<=s.bp?i:void 0},get fitPadTopBase(){let t=ka(e.tubeMapGenes);return F+Math.max(0,t-1)*ya+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 r=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-this.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+F<=a?1/0:0:(a-m-F)/t.h,c=Math.min(i(n+2*Ae),s(r));return Math.min(i(F),s(r+o+Ae))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+Ae:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(F,e.legendSize.width+2*Ae):F},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(yi/o,(this.paneCeiling-this.fitPadTop-F)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facet;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.facet;return t?Ct(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?Pt({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=this.layoutBounds,n=e.paneWidth-F-this.fitPadRight,o=this.paneCeiling;if(!t)return o;let r=this.facetGrid;if(r)return Math.max(Xt,r.total);let a=Math.max(Xt,e.legendSize.height+2*Ae+e.referenceStripZonePx);return e.pixelRows?Math.min(o,Math.max(a,t.h+this.fitPadTop+F)):t.w>0&&n>0?Math.min(o,Math.max(a,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+F)):o},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=this.layoutBounds,n=this.facetGrid;return t?n?Ne(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):Ne(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:this.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return Un(ot(e),Ti)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:o,selectedNode:r}=e,a=new Map;r!==null&&a.set(r,Li),n!==null&&n!==r&&a.set(n,to),t.setNodeHighlights(a),t.setEdgeHighlight(o,to)},paint(t){let n=ea();t.updateTransform({scaleX:e.scaleX*n,scaleY:e.scaleY*n,translateX:e.translateX*n,translateY:e.translateY*n,dpr:n}),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?Ut:Yt)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:i}=e;if(!o||!r||!a||!i)return;le(e.viewportDirty,e.positionsVersion);let s=(0,Go.untracked)(()=>e.viewportToBuild());return{batch:Et({...at(a,i,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:r,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:(0,Go.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:s,referenceRamp:e.referenceRamp,version:e.positionsVersion}),viewportBounds:s}},get overlayLabels(){return da(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?ia(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,r=t&&`${t.refName}:${t.start}-${t.end}`,a=Ie(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ie(n.gbzDbLocation):void 0,s=a?{gfa:a,region:r}:i&&t&&r?{gbz:{db:i,index:Ie(n.haplotypeIndexLocation),region:r,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(!s)return;let c=e.showGenes?e.geneTrack:void 0,d=c?(0,hs.getSession)(e).tracks.find(p=>p.trackId===c.trackId):void 0,m=d?(0,on.expandTabixShorthand)((0,on.readConfObject)(d,"adapter"),"gffGzLocation"):void 0,l=m?.type==="Gff3TabixAdapter"?{file:Ie(m.gffGzLocation),index:Ie(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:l?.file&&l.index?l:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...mo({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.colorDomain}),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\u2026 to None first":e.drawsNodes||e.walkRowBars?void 0:`${H(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?e.popStack.length?"A spec names the whole graph, so go back out of this bubble 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cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?he(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,mt.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,ue.getSession)(e).tracks.filter(n=>(0,mt.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,mt.readConfObject)(n,"name"),adapterType:(0,mt.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>pt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Mo.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Qi(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return Qt(e.geneTrackChoices,e.geneTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?gn(e.graph):void 0},get cutWalkRows(){return e.graph?Mt(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=(0,ue.getSession)(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(i=>r[i]??[])]}},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;try{t=(0,ue.getContainingView)(e)}catch{return}let n=Ji(t,e.geneTrack?.trackId);return n.length?new rs.default({filters:n,jexl:(0,ue.getEnv)(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?en(n?t.filter(o=>n.passes(o)):t):void 0}})).views(e=>({get backboneGenes(){let{backbone:t,geneAssembly:n,geneFeatures:o}=e,r=e.drawsLoadedReference||n!==void 0&&fn(t,[n])!==void 0;return 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n&&r&&o.size>0?n.map((a,i)=>o.has(r[i]?.name??"")?a:Lr):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:o}=e;return n&&o?be({nodeId:t,nodeById:n,neighbors:o}):void 0}})).views(e=>({get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&Mn(t.length)?je(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?e.nodeSpan(t):n?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return t&&n?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var To=y(q(),1);function Q(e){return typeof e=="object"&&e!==null}function Wd(e){return Q(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function lt(e){return e.flatMap(t=>Q(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function gt({views:e,connectedViewId:t,assemblyName:n}){let o=lt(e).filter(a=>Wd(a)).filter(a=>a.assemblyNames.includes(n));return o.find(a=>a.id===t)??(o.length===1?o[0]:void 0)}function ht(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function ss(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var Hd=1e3;function vo(e,t=Hd){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function cs(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function ds({session:e,location:t,assembly:n,connectedViewId:o,tracks:r=[]}){let a=gt({views:e.views,connectedViewId:o,assemblyName:n}),i;return a?(ss(e,`Could not show ${n} ${Ke(t)}`,Promise.resolve(a.navToLocString(Ot(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${Ke(t)}`,init:{assembly:n,loc:Ot(t),tracks:r}}).id,i}function ps({session:e,location:t,assembly:n,connectedViewId:o}){let r=gt({views:e.views,connectedViewId:o,assemblyName:n});return r&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n}),r!==void 0}function is(e,t){if(t===void 0)return[];let n=e.tracks.find(r=>(0,To.readConfObject)(r,"trackId")===t),o=n?(0,To.readConfObject)(n,"assemblyNames"):[];return Array.isArray(o)?o.filter(r=>typeof r=="string").map(r=>ht(e,r)):[]}function us({session:e,contributors:t,trackId:n,graphTrackId:o}){let r=is(e,o),a=is(e,n),i=t.filter(d=>a.includes(d.sample)),s=i.length>=2?i:t,c={init:{views:s.map(d=>({assembly:d.sample,loc:Ot(d),...o!==void 0&&r.includes(d.sample)?{tracks:[o]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?ss(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c)):e.addView("LinearSyntenyView",c)}var ms=as.views(e=>({get contributingAssemblies(){let t=e.graph,n=t?tr(t):[];return t?va(t,{maxGap:n.length>0?rr(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,Me.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([a,i])=>[i,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(0,Me.getSession)(e).tracks){let o=(0,nn.readConfObject)(n,"adapter").type;if(!pt.has(o))continue;let r={trackId:n.trackId,name:(0,nn.readConfObject)(n,"name"),adapterType:o};for(let a of(0,nn.readConfObject)(n,"assemblyNames")){let i=ht((0,Me.getSession)(e),a);t.set(i,[...t.get(i)??[],r])}}return new Map([...t].flatMap(([n,o])=>{let r=Qt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return Ga(cs(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&gt({views:[...(0,Me.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?Ye(n):void 0,r=o?Ue(e.assemblyResolver,o):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,c=a&&i&&s?be({nodeId:t,nodeById:i,neighbors:s}):void 0,d=a&&c?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...c}:void 0;return{own:o&&r?{location:vo(o),assembly:r}:void 0,reference:a&&d?{location:vo(d),assembly:a.assemblyName}:void 0,highlight:a&&d?{location:d,assembly:a.assemblyName}:void 0}}})).views(e=>({get host(){let t;try{t=(0,Me.getContainingView)(e)}catch{return}return zi(t)?t:void 0}}));var ls=ms.views(e=>({get walkStripShown(){return Ur({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,popped:e.popStack.length>0,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 $t(t,{width:e.paneWidth})},get cutsWholeWalks(){return Kr(H(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?qr(e.graph,[t.reference,...t.rows],o):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Vt(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,r=0;for(let a of t.rows){if(!a.axis){r++;continue}let i=Ue(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){o++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...Pn(a.axis,a.bp)}})}return{reads:n.slice(0,no),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-no)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let r=o.haplotype===void 0?void 0:`${o.sample}#${o.haplotype}`,a=t===0?e.graphRegion?.assemblyName:Ue(e.assemblyResolver,{sample:o.sample,haplotype:r});return{label:o.label,assembly:a,location:{sample:o.sample,haplotype:r,refName:o.axis.contig,...Pn(o.axis,o.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?zr([t.reference,...t.rows],n):void 0}}));var gs=ls.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&H(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 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e.showReferenceStrip&&e.referenceStripApplies&&t?Ra(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?dt(t,n):void 0}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.referenceStripFrame!==void 0},get referenceStripOverhangs(){let t=e.referenceStripFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:o}=xa(e.referenceStripBlocks,t,e.paneWidth);return n>0||o>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=a=>({x:a.x*e.scaleX+e.translateX,y:a.y*e.scaleY+e.translateY}),n=e.hoveredNode===null?e.hoveredBubble:null;if(n){let a=e.bubbleHalos.find(i=>Or(i.bubble,n));return{start:n.start,end:n.end,anchor:a?t(a.labelAt):void 0}}let o=e.hoveredNode??e.selectedNode,r=o===null?void 0:e.nodeSpan(o);return r&&o!==null?{...r,anchor:Vt(e.nodePositions?.[o],t)}:void 0},referenceStripNodeAt(t,n){let o=e.referenceStripFrame;return e.referenceStripShown&&o?La(e.referenceStripBlocks,o,t,n):void 0},get paperCss(){return wi(e.darkMode?Ut:Yt)},get referenceStripZonePx(){return e.referenceStripShown?Sa:0}}));function jd(e,t,n){if(!(!e||!t))return Xr(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var fs=gs.views(e=>({get paneCeiling(){return Math.max(Xt,e.paneHeight??bi)},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=e.host?this.canvasHeight:this.paneCeiling,o=(e.walkRowGroups?.sections.length??0)*Er;return Yr(t.rows.length+1,n-this.fitPadTopBase-F-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?Vr(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return jd(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=Xe(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,r)=>({...o,y:t.rowY(r)})):n},get fitPadLeft(){return Math.max(F,...this.drawnRowLabels.map(t=>gr(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ze(n,this.walkRowPitch):void 0;return t?tt(t,{region:e.popStack.length===0?e.graphRegion:void 0,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,r=o?t.reference:t.rows.find(a=>a.name===n);return r?{label:r.label,readout:jr(r,o?void 0:t.reference,t.unit,r.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,r=this.walkRowPitch,a=this.walkRowPlacement;if(!o||!r||!a)return;let i=a.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),s=[o.reference,...o.rows][i],c=a.rowY(i)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return s&&Math.abs(n-c)<=r.barPx/2+2&&d>=0&&d<=s.bp?i:void 0},get fitPadTopBase(){let t=ka(e.tubeMapGenes);return F+Math.max(0,t-1)*ya+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 r=this.fitPadTopBase,a=e.host?this.canvasHeight:this.paneCeiling,i=m=>(e.paneWidth-this.fitPadLeft-m)/t.w,s=m=>e.pixelRows?t.h+m+F<=a?1/0:0:(a-m-F)/t.h,c=Math.min(i(n+2*Ae),s(r));return Math.min(i(F),s(r+o+Ae))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+Ae:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(F,e.legendSize.width+2*Ae):F},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(yi/o,(this.paneCeiling-this.fitPadTop-F)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facet;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.facet;return t?Ct(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?Pt({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facet.columns}):void 0},get facetGrid(){return this.facetGridIn(e.host?this.canvasHeight:this.paneCeiling)},get canvasHeight(){let t=this.layoutBounds,n=e.paneWidth-F-this.fitPadRight,o=this.paneCeiling;if(!t)return o;let r=this.facetGrid;if(r)return Math.max(Xt,r.total);let a=Math.max(Xt,e.legendSize.height+2*Ae+e.referenceStripZonePx);return e.pixelRows?Math.min(o,Math.max(a,t.h+this.fitPadTop+F)):t.w>0&&n>0?Math.min(o,Math.max(a,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+F)):o},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=this.layoutBounds,n=this.facetGrid;return t?n?Ne(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):Ne(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:this.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return Un(ot(e),Ti)},applyHighlights(t){let{hoveredNode:n,hoveredEdge:o,selectedNode:r}=e,a=new Map;r!==null&&a.set(r,Li),n!==null&&n!==r&&a.set(n,to),t.setNodeHighlights(a),t.setEdgeHighlight(o,to)},paint(t){let n=ea();t.updateTransform({scaleX:e.scaleX*n,scaleY:e.scaleY*n,translateX:e.translateX*n,translateY:e.translateY*n,dpr:n}),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?Ut:Yt)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:i}=e;if(!o||!r||!a||!i)return;le(e.viewportDirty,e.positionsVersion);let s=(0,Go.untracked)(()=>e.viewportToBuild());return{batch:Et({...at(a,i,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:r,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:(0,Go.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:s,referenceRamp:e.referenceRamp,version:e.positionsVersion}),viewportBounds:s}},get overlayLabels(){return da(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?ia(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,r=t&&`${t.refName}:${t.start}-${t.end}`,a=Ie(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ie(n.gbzDbLocation):void 0,s=a?{gfa:a,region:r}:i&&t&&r?{gbz:{db:i,index:Ie(n.haplotypeIndexLocation),region:r,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(!s)return;let c=e.showGenes?e.geneTrack:void 0,d=c?(0,hs.getSession)(e).tracks.find(p=>p.trackId===c.trackId):void 0,m=d?(0,on.expandTabixShorthand)((0,on.readConfObject)(d,"adapter"),"gffGzLocation"):void 0,l=m?.type==="Gff3TabixAdapter"?{file:Ie(m.gffGzLocation),index:Ie(m.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:l?.file&&l.index?l:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...mo({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.colorDomain}),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\u2026 to None first":e.drawsNodes||e.walkRowBars?void 0:`${H(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?e.popStack.length?"A spec names the whole graph, so go back out of this bubble first":this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base track or a GFA url":`bandage-figure draws no ${H(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?uo(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.colorDomain,fitToDrawing:e.popStack.length>0,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:this.figureSpecUnavailable?void 0:this.figureSpec()}):void 0},get tubeMapFrame(){let t=e.layoutResult?.tubeMap;return t?lo(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-F}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX?ua(t):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapReferenceNodes,n=e.tubeMapFrame,{host:o,graphRegion:r}=e,a=t&&n&&o?.initialized&&r?dt(o,r):void 0;return t&&n&&a?la(t,i=>i*a.scale+a.translateX,n.x,e.paneWidth):[]}})).views(e=>({get tubeMapKeys(){let t=e.layoutResult,n=t?.tubeMap?.layout.reads??[],o=e.tubeMapPicture,r=e.tubeMapFrame,a=o&&r&&fa(r.yScale)?o.mismatches.filter(i=>ba(i,{x:r.x,width:e.paneWidth})):[];return{logWidths:t?.tubeMap!==void 0&&!t.referenceAxis,foldBp:e.tubeMapDeviations.length>0?e.tubeMapFold:void 0,forwardReads:n.some(i=>!i.is_reverse),reverseReads:n.some(i=>i.is_reverse),mismatches:new Set(a.map(i=>i.kind))}},tubeMapNodeAt(t,n){let o=e.layoutResult?.tubeMap,r=e.tubeMapFrame;return(o&&r?go(o,r,t,n):null)??ga(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));var bs=fs.actions(e=>({setError(t){e.error=t,e.isLoading=!1,e.statusMessage=""},finishLoading(){e.isLoading=!1,e.statusMessage=""},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,n,o){e.lastGeometryMs=t,e.lastGeometryStrokeCount=n,e.builtViewport={...o,viewportDirty:e.viewportDirty},e.geometryVersion++},markPainted(){e.paintedViewport=e.builtViewport},setLayoutQuality(t){e.layoutQuality=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.layoutMode=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let 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n=e.walkLayers;e.walkLayers=n.some(o=>o.walk===t)?n.filter(o=>o.walk!==t):[...n,{walk:t}]},setWalkColor(t,n){e.walkLayers=e.walkLayers.map(o=>o.walk===t?{...o,color:{...o.color,...n}}:o)},setPaneHeight(t){e.paneHeight=t},setWalkRowSamples(t){e.walkRowSamples=t},setWalkRowGroupBy(t){e.walkRowGroupBy=t},setWalkRowSampleTable(t){e.walkRowSampleTable=t},pairWithLinearView(t){let n=e.connectedViewId;n!==void 0&&lt([...(0,ft.getSession)(e).views]).some(r=>r.id===n)||(e.connectedViewId=t)},setHoveredNode(t){e.hoveredNode=t},setHoveredRowWalks(t){t.join(`
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e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,Y.addDisposer)(e,(0,Bs.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!H(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var np=(0,$s.defineLaunchKeys)()({});function Eo(e){e.addViewType(()=>new Ds.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Io(),launchKeys:np,ReactComponent:(0,Fs.lazy)(()=>import("./chunks/GraphGenomeView-5OPCROMQ.js"))}))}var Vs=y(q(),1),Ee=y(ge(),1),Bo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function op(e){let t=e.getElementTypesInGroup("display"),n=r=>t.find(a=>a.name===r),o=r=>r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Bo.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Fo(e){e.addTrackType(()=>{let 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mn=(e,t)=>(0,ln.ConfigurationSchema)(e,{indexType:{model:uc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ip=(0,ln.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:mn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:mn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),sp=(0,ln.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:mn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:mn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ip},{explicitlyTyped:!0,preProcessSnapshot:jo}),mc=sp;function zo(e){e.addAdapterType(()=>new lc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:jo,configSchema:mc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-3BFNY4SB.js").then(t=>t.default)}))}var cp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function dp(e){return ar(e).toLowerCase().endsWith(".gbz.db")}function pp(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function up(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&dp(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&ir(e))return sr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Xo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",pp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>up(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>cp.has(n)?"GraphTrack":t(n,o))}var bc=y(ae(),1),wc=y(Ic(),1),Yo=y(Cc(),1),yc=y(Ec(),1);function gc(e){let t;if(Q(e)){let{refName:n,start:o,end:r,assemblyName:a}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof a=="string"?a:void 0})}return t}function mp(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function hc(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function lp(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(o=>Q(o)&&o.type==="LinearGraphDisplay"):[])}function fc(e,t,n){let o=[],r=lt(e),a=new Set(r.map(i=>Q(i)?i.id:void 0));for(let i of r){if(Q(i)&&i.id===t)for(let s of lp(i)){let c=gc(s.hoverHighlight);c&&hc(c,n)&&o.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&mp(i,t,a)){let s=gc(i.hoverHighlight);s&&hc(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var Be=y(De(),1),gp=(0,yc.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,wc.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),hp=(0,Yo.observer)(function({model:t,region:n}){let{classes:o}=gp(),r=t.getHighlightCoords(n);return r?(0,Be.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),fp=(0,Yo.observer)(function({model:t}){let{views:n}=(0,bc.getSession)(t);return(0,Be.jsx)(Be.Fragment,{children:fc([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,Be.jsx)(hp,{model:t,region:r},`graph-hover-${o}`))})}),kc=fp;var Sc=y(De(),1),bp="LinearGenomeView-TracksContainerComponent";function Uo(e){e.contributeToExtensionPoint(bp,({model:t})=>(0,Sc.jsx)(kc,{model:t},"graphgenomeview-hover-highlight"))}var Rc=y(ge(),1);function wp(e){return e.views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)}}))}function Ko(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Rc.DisplayType&&Bo.includes(t.name)&&t.extendStateModel(wp),t))}var xc="GraphGenomeView";var Lc="6.2.0";var qo=class extends Mc.default{constructor(){super(...arguments);this.name=xc;this.version=Lc}install(n){Eo(n),Oo(n),Fo(n),Do(n),Uo(n),zo(n),Ho(n),Dn(n),Vn(n),Xo(n),Ko(n),n.addRpcMethod(()=>new Ze(n)),n.addRpcMethod(()=>new Je(n)),n.addRpcMethod(()=>new qe(n))}configure(n){try{(0,Tc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Wt,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{qo as default};
+`).then(()=>{o.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(r=>{o.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},launchMenuItems(){let t=[];for(let n of Aa({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:o=>{e.showInLinearView(o)},onShowSynteny:o=>{e.showSyntenyView(o)}}))(0,Ps.pushLaunchViewMenuItem)(t,n);return t}}));function cn(){return Ns}var No=y(q(),1);function Cs(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function Co(e){let t=(0,No.readConfObject)(e,"assemblyNames"),n=Cs(t)?t.slice(1):[];return n.length>0?n:void 0}function dn(e){let t=(0,No.readConfObject)(e,"assemblyNames");return Cs(t)?t[0]:void 0}function pn(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function tp(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function Io(){return Y.types.compose("GraphGenomeView",Is.BaseViewModel,cn(),Y.types.model({type:Y.types.literal("GraphGenomeView"),gfaLocation:Y.types.maybe(Y.types.frozen()),loadedRegion:Y.types.maybe(Y.types.frozen()),loadedTrackId:Y.types.optional(Y.types.string,""),subgraphContext:Y.types.optional(Y.types.number,1),subgraphHaplotypes:Y.types.maybe(Y.types.frozen()),maxRegionBp:Y.types.optional(Y.types.number,nt)})).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,Es.getSession)(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return e.launchMenuItems()}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(tp(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let o=e.sourceTrack,r=n.end-n.start,a=o?pn(dn(o),n.assemblyName):void 0;if(!o)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(r>e.maxRegionBp)e.setError(new Error(`Region too large (${Re(r)}) \u2014 zoom in to view graph (max ${Re(e.maxRegionBp)})`));else return e.cutSubgraph(he(e,o),n,{hops:e.subgraphContext,haplotypes:e.subgraphHaplotypes,...e.cutsWholeWalks?{snarls:"overlapping"}:{}})}}}).actions(e=>({retryLoad(){e.load()},switchLayout(t){let n=e.cutsWholeWalks;return e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,Y.addDisposer)(e,(0,Bs.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!H(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var np=(0,$s.defineLaunchKeys)()({});function Eo(e){e.addViewType(()=>new Ds.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Io(),launchKeys:np,ReactComponent:(0,Fs.lazy)(()=>import("./chunks/GraphGenomeView-6CRBLHNG.js"))}))}var Vs=y(q(),1),Ee=y(ge(),1),Bo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function op(e){let t=e.getElementTypesInGroup("display"),n=r=>t.find(a=>a.name===r),o=r=>r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Bo.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Fo(e){e.addTrackType(()=>{let t=(0,Vs.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ee.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ee.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ee.createBaseTrackModel)(e,"GraphTrack",t)});for(let o of op(e))n.addDisplayType(o);return n})}function Do(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...o}=t;return n.addView("GraphGenomeView",o),t})}var rc=y($e(),1),ac=y(_s(),1);var js=y(q(),1),zs=y(Hs(),1),$o=y(ne(),1);function Xs(){return(0,js.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:$o.types.enumeration("LayoutMode",Tt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:$o.types.enumeration("ColorScheme",vt),defaultValue:"auto"},...(0,zs.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Qs=y($e(),1);var wt=y(q(),1),ec=y(ge(),1),tc=y(cr(),1),Vo=y(ae(),1),nc=y(Us(),1),C=y(ne(),1),un=y(qs(),1);var bt=y(St(),1);function Js(e){return e instanceof Error&&(e.name==="NodeLimitError"||e.regionTooLarge===!0||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Zs(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var rp=(0,Qs.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-2QQYWNWW.js"));function oc(e){return C.types.compose("LinearGraphDisplay",ec.BaseDisplay,(0,nc.default)(),cn(),C.types.model({type:C.types.literal("LinearGraphDisplay"),configuration:(0,wt.ConfigurationReference)(e),pane:C.types.maybe(C.types.frozen()),overviewRowsChoice:C.types.maybe(C.types.frozen()),overviewRowOrder:C.types.maybe(C.types.frozen()),cutRegion:C.types.maybe(C.types.frozen()),coarseCut:C.types.optional(C.types.boolean,!1),maxRegionBp:C.types.optional(C.types.number,nt),subgraphContext:C.types.optional(C.types.number,1),subgraphHaplotypes:C.types.maybe(C.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,overviewRowsChoice:o,overviewRowOrder:r,...a}=t;if(!n)return a;let{type:i,...s}=n;return{...s,...a}}).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0})).views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,wt.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,wt.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??Co(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let o=t.adapterConfig.coarse?.aboveBpPerPx;return typeof o=="number"?o:void 0}})).views(t=>({tierAt(n){let o=t.coarseAboveBpPerPx;return o!==void 0&&n>o?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${Re(n.end-n.start)}, max ${Re(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,un.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,un.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n,t.dense=void 0},setDense(n){t.dense=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let o=pn(dn(t.parentTrack.configuration),n.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let r=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:r?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:r?"coarse":void 0,...H(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let o=t.tierAt(n.bpPerPx);return t.coarseCut=o==="coarse",t.cutRegion=ho(n,t.capFor(o),H(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let o=H(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||Zs(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Yi(t.cutRegion,n,o)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,C.isAlive)(t)&&Js(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let o=H(t.chosenLayoutMode);t.setLayoutMode(n);let r=H(n),a=t.host?Jt(t.host):void 0;return a&&!t.regionTooLarge&&(r.cutMargins!==o.cutMargins||r.wholeWalks!==o.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,C.addDisposer)(t,(0,bt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,C.addDisposer)(t,(0,bt.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,o)=>n?.scale===o?.scale&&n?.translateX===o?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,C.addDisposer)(t,(0,bt.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,C.addDisposer)(t,(0,bt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:o}=t,r=n&&o?Jt(o):void 0;r&&t.settleOn(r)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Jt(t.host):void 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graph",checked:o?o.length===0:!n,onClick:()=>{r([])}},...n?[{type:"radio",label:`The track's ${n.length} assemblies`,checked:o===void 0,onClick:()=>{r(void 0)}}]:[],{type:"radio",label:"Chosen in Settings...",checked:(o?.length??0)>0,onClick:()=>{this.openSettings()}}]}]},openSettings(){(0,Vo.getSession)(t).queueDialog(n=>[rp,{model:t,open:!0,onClose:n}])},trackMenuItems(){let n=t.launchMenuItems();return(0,tc.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Wt,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...this.haplotypeMenuItems(),...t.graphMenuItems(),{label:"Settings",icon:Pa,onClick:()=>{this.openSettings()}},...n]}}))}function Oo(e){e.addDisplayType(()=>{let t=Xs();return Object.assign(new ac.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:oc(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,rc.lazy)(()=>import("./chunks/LinearGraphDisplay-KNEXJAAV.js"))}),{adapterCapabilities:["getSubgraph"]})})}var cc=y(Ht(),1);var _o=y(q(),1),ic=y(ne(),1);function Wo(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:o?"CSI":"TBI",location:{uri:`${t}.${o?"csi":"tbi"}`,baseUri:n}}}:e}var ap=(0,_o.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,_o.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:ic.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Wo}),sc=ap;function Ho(e){e.addAdapterType(()=>new cc.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Wo,configSchema:sc,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-MQRO5J7Z.js").then(t=>t.default)}))}var lc=y(Ht(),1);var ln=y(q(),1),uc=y(ne(),1);function dc(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function pc(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:dc(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:dc(`${t}.links.bed.gz`,n,o)}:e}function jo(e){let{coarse:t,baseUri:n}=e;return pc(typeof t=="object"&&t!==null?{...e,coarse:pc({baseUri:n,...t})}:e)}var mn=(e,t)=>(0,ln.ConfigurationSchema)(e,{indexType:{model:uc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ip=(0,ln.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:mn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:mn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),sp=(0,ln.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:mn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:mn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ip},{explicitlyTyped:!0,preProcessSnapshot:jo}),mc=sp;function zo(e){e.addAdapterType(()=>new lc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:jo,configSchema:mc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-ALEXRTPS.js").then(t=>t.default)}))}var cp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function dp(e){return ar(e).toLowerCase().endsWith(".gbz.db")}function pp(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function up(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&dp(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&ir(e))return sr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Xo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",pp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>up(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>cp.has(n)?"GraphTrack":t(n,o))}var bc=y(ae(),1),wc=y(Ic(),1),Yo=y(Cc(),1),yc=y(Ec(),1);function gc(e){let t;if(Q(e)){let{refName:n,start:o,end:r,assemblyName:a}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof a=="string"?a:void 0})}return t}function mp(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function hc(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function lp(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>Q(n)&&Array.isArray(n.displays)?n.displays.filter(o=>Q(o)&&o.type==="LinearGraphDisplay"):[])}function fc(e,t,n){let o=[],r=lt(e),a=new Set(r.map(i=>Q(i)?i.id:void 0));for(let i of r){if(Q(i)&&i.id===t)for(let s of lp(i)){let c=gc(s.hoverHighlight);c&&hc(c,n)&&o.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&mp(i,t,a)){let s=gc(i.hoverHighlight);s&&hc(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var Be=y(De(),1),gp=(0,yc.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,wc.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),hp=(0,Yo.observer)(function({model:t,region:n}){let{classes:o}=gp(),r=t.getHighlightCoords(n);return r?(0,Be.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),fp=(0,Yo.observer)(function({model:t}){let{views:n}=(0,bc.getSession)(t);return(0,Be.jsx)(Be.Fragment,{children:fc([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,Be.jsx)(hp,{model:t,region:r},`graph-hover-${o}`))})}),kc=fp;var Sc=y(De(),1),bp="LinearGenomeView-TracksContainerComponent";function Uo(e){e.contributeToExtensionPoint(bp,({model:t})=>(0,Sc.jsx)(kc,{model:t},"graphgenomeview-hover-highlight"))}var Rc=y(ge(),1);function wp(e){return e.views(t=>({get adapterConfig(){return he(t,t.parentTrack.configuration)}}))}function Ko(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Rc.DisplayType&&Bo.includes(t.name)&&t.extendStateModel(wp),t))}var xc="GraphGenomeView";var Lc="6.3.0";var qo=class extends Mc.default{constructor(){super(...arguments);this.name=xc;this.version=Lc}install(n){Eo(n),Oo(n),Fo(n),Do(n),Uo(n),zo(n),Ho(n),Dn(n),Vn(n),Xo(n),Ko(n),n.addRpcMethod(()=>new Ze(n)),n.addRpcMethod(()=>new Je(n)),n.addRpcMethod(()=>new qe(n))}configure(n){try{(0,Tc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Wt,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{qo as default};
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