npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.3.1 → 6.4.0 - Mend

jbrowse-plugin-graphgenomeviewer 6.3.1 → 6.4.0

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

@@ -1,9 +1,9 @@
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e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!so(e))},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Sr(e.chosenLayoutMode,e.graph):!1},get canAnchorLayout(){return e.graph?.nodes.some(t=>t.stable?.rank===0)??!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?ze(t):[]},get effectiveDrawPaths(){return e.drawPaths&&Gn(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){return e.colorDomain??e.graphRegion},get walkRamp(){let{graph:t}=e;return t&&e.walkLayers.some(n=>n.color?.field==="reference")?Ae(t,this.rampDomain):void 0},get modeDrawsNodes(){return O(e.chosenLayoutMode).drawsNodes},get liftedWalkLayers(){return e.walkLayers.length>0||!this.modeDrawsNodes?e.walkLayers:e.hoveredRowWalks.map(t=>({walk:t}))},get walkLift(){let{graph:t}=e,n=this.liftedWalkLayers;return t&&n.length>0&&!e.layoutResult?.tubeMap?dt(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facet.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?pt(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!Ee.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Lt(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){for(let t of this.walkLift?.walks??[])if(t.encoding.field!=="walk"){for(let n of t.colors.values())if(n===$r)return!0}return!1},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":Pt(e.chosenColorScheme,e.graph)},get tubeMapReads(){return(e.layoutResult?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each lifted walk colours its own lane: set it under the menu, Walk, Colour"}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get rowLabels(){return e.layoutResult?.rowLabels??[]},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?So(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?we(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,gt.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,ge.getSession)(e).tracks.filter(n=>(0,gt.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,gt.readConfObject)(n,"name"),adapterType:(0,gt.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>mt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Go.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return ds(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return tn(e.geneTrackChoices,e.geneTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?bn(e.graph):void 0},get cutWalkRows(){return e.graph?vt(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=(0,ge.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,ge.getContainingView)(e)}catch{return}let n=ss(t,e.geneTrack?.trackId);return n.length?new gs.default({filters:n,jexl:(0,ge.getEnv)(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?nn(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&&yn(t,[n])!==void 0;return t&&o&&r?Sn(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?_e(e.drawnGraph):void 0},get nodeInk(){return Bt(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?ke(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=t?vt(e.graph,t,t.unit):e.cutWalkRows;if(!n)return;let[o,...r]=La([n.reference,...n.rows],t?.calls);return{...n,reference:o,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&&(!("uri"in t)||t.uri)?t:void 0},get walkRowGroupFields(){return Pr(e.walkRowSampleTable)},get walkRowGroups(){let t=this.cohortWalkRows,n=e.walkRowSampleTable,o=e.walkRowGroupBy;return t&&n&&o&&this.walkRowGroupFields.includes(o.field)?Nr(Pe(t.rows,e.walkRowSamples),n,o):void 0},get walkRowBars(){let t=this.cohortWalkRows;return t?{...t,rows:this.walkRowGroups?.rows??Pe(t.rows,e.walkRowSamples)}:void 0},get drawsNodes(){return!e.layoutResult?.tubeMap&&!this.walkRowBars},get genePins(){he(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?ct(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){he(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:ko(e.graph,e.bubbles,t,n=>e.walkLabel(n),e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Ae(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return xe(e.scale,e.pixelRows).scaleX},get scaleY(){return xe(e.scale,e.pixelRows).scaleY},get axisScale(){return xe(e.scale,e.pixelRows)}})).views(e=>({get deletionDrawing(){return e.graph?We(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?xo(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>br(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:Er):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:o}=e;return n&&o?ye({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&&Gn(t.length)?ze(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&&e.chosenHighlightOnHover?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var Po=b(q(),1);function Q(e){return typeof e=="object"&&e!==null}function np(e){return Q(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function ht(e){return e.flatMap(t=>Q(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function ft({views:e,connectedViewId:t,assemblyName:n}){let o=ht(e).filter(a=>np(a)).filter(a=>a.assemblyNames.includes(n));return o.find(a=>a.id===t)??(o.length===1?o[0]:void 0)}function bt(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function bs(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var op=1e3;function Ao(e,t=op){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 ws(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 ys({session:e,location:t,assembly:n,connectedViewId:o,tracks:r=[]}){let a=ft({views:e.views,connectedViewId:o,assemblyName:n}),i;return a?(bs(e,`Could not show ${n} ${Je(t)}`,Promise.resolve(a.navToLocString(_t(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${Je(t)}`,init:{assembly:n,loc:_t(t),tracks:r}}).id,i}function ks({session:e,location:t,assembly:n,connectedViewId:o}){let r=ft({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 fs(e,t){if(t===void 0)return[];let n=e.tracks.find(r=>(0,Po.readConfObject)(r,"trackId")===t),o=n?(0,Po.readConfObject)(n,"assemblyNames"):[];return Array.isArray(o)?o.filter(r=>typeof r=="string").map(r=>bt(e,r)):[]}function Ss({session:e,contributors:t,trackId:n,graphTrackId:o}){let r=fs(e,o),a=fs(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:_t(d),...o!==void 0&&r.includes(d.sample)?{tracks:[o]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?bs(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c)):e.addView("LinearSyntenyView",c)}var xs=hs.views(e=>({get contributingAssemblies(){let t=e.graph,n=t?or(t):[];return t?va(t,{maxGap:n.length>0?ir(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,Te.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,Te.getSession)(e).tracks){let o=(0,rn.readConfObject)(n,"adapter").type;if(!mt.has(o))continue;let r={trackId:n.trackId,name:(0,rn.readConfObject)(n,"name"),adapterType:o};for(let a of(0,rn.readConfObject)(n,"assemblyNames")){let i=bt((0,Te.getSession)(e),a);t.set(i,[...t.get(i)??[],r])}}return new Map([...t].flatMap(([n,o])=>{let r=tn(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return Ta(ws(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&ft({views:[...(0,Te.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?Ke(n):void 0,r=o?qe(e.assemblyResolver,o):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,c=a&&i&&s?ye({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:Ao(o),assembly:r}:void 0,reference:a&&d?{location:Ao(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,Te.getContainingView)(e)}catch{return}return ts(t)?t:void 0}}));var Rs=xs.views(e=>({get walkStripShown(){return Yr({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:Pe(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Vt(t,{width:e.paneWidth})},get cutsWholeWalks(){return Ur(O(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?Kr(e.graph,[t.reference,...t.rows],o):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Ot(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=qe(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){o++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...En(a.axis,a.bp)}})}return{reads:n.slice(0,ao),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-ao)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let r=o.haplotype===void 0?void 0:`${o.sample}#${o.haplotype}`,a=t===0?e.graphRegion?.assemblyName:qe(e.assemblyResolver,{sample:o.sample,haplotype:r});return{label:o.label,assembly:a,location:{sample:o.sample,haplotype:r,refName:o.axis.contig,...En(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?jr([t.reference,...t.rows],n):void 0}}));var Ms=Rs.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&O(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?ut(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?ga(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?da(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?Ma(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?ua(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?ba(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;return e.showReferenceStrip&&e.referenceStripApplies&&t?Sa(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?ut(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=>Vr(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:Ot(e.nodePositions?.[o],t)}:void 0},referenceStripNodeAt(t,n){let o=e.referenceStripFrame;return e.referenceStripShown&&o?Ra(e.referenceStripBlocks,o,t,n):void 0},get paperCss(){return vi(e.darkMode?qt:Kt)},get referenceStripZonePx(){return e.referenceStripShown?ka:0}}));function rp(e,t,n){if(!(!e||!t))return Xr(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var vs=Ms.views(e=>({get paneCeiling(){return Math.max(Ut,e.paneHeight??Li)},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=e.host?this.canvasHeight:this.paneCeiling,o=(e.walkRowGroups?.sections.length??0)*Tr;return zr(t.rows.length+1,n-this.fitPadTopBase-F-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?Ir(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return rp(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=Ue(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=>fr(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?Ye(n,this.walkRowPitch):void 0;return t?ot(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:Wr(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=ya(e.tubeMapGenes);return F+Math.max(0,t-1)*wa+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*Ne),s(r));return Math.min(i(F),s(r+o+Ne))>=c?"top":"right"},get fitPadTop(){return 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Vn=f(K(),1),On=f(ne(),1),Uc=(0,Vn.ConfigurationSchema)("GbzBaseSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},gbzDbLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.gbz.db",locationType:"UriLocation"}},haplotypeIndexLocation:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}},readsLocation:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}},readsIndex:(0,Vn.ConfigurationSchema)("GbzBaseReadsIndex",{indexType:{model:On.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}}}),samplesTsvLocation:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}},subgraphSnarls:{type:"stringEnum",model:On.types.enumeration("SnarlOutput",["none","contained","overlapping"]),defaultValue:kt.snarls},referenceSample:{type:"string",defaultValue:""},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},context:{type:"number",defaultValue:kt.context,advanced:!0},nodeLimit:{type:"number",defaultValue:kt.limit,advanced:!0}},{explicitlyTyped:!0,preProcessSnapshot:e=>{let{uri:t,baseUri:n,reads:o}=e;return{...e,...t?{gbzDbLocation:{uri:t,baseUri:n}}:{},...typeof 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e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":Gt(e.chosenColorScheme,e.graph)},get tubeMapReads(){return(e.layoutResult?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each lifted walk colours its own lane: set it under the menu, Walk, Colour"}: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 rowLabels(){return e.layoutResult?.rowLabels??[]},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 poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?yo(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?be(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?(0,lt.readConfObject)(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?(0,le.getSession)(e).tracks.filter(n=>(0,lt.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,lt.readConfObject)(n,"name"),adapterType:(0,lt.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>ut.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>vo.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return as(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return en(e.geneTrackChoices,e.geneTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?fn(e.graph):void 0},get cutWalkRows(){return e.graph?Lt(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=(0,le.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,le.getContainingView)(e)}catch{return}let n=os(t,e.geneTrack?.trackId);return n.length?new ps.default({filters:n,jexl:(0,le.getEnv)(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?tn(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&&wn(t,[n])!==void 0;return t&&o&&r?kn(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?_e(e.drawnGraph):void 0},get nodeInk(){return Et(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?ye(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=t?Lt(e.graph,t,t.unit):e.cutWalkRows;if(!n)return;let[o,...r]=Ma([n.reference,...n.rows],t?.calls);return{...n,reference:o,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new 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e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Pe(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return Se(e.scale,e.pixelRows).scaleX},get scaleY(){return Se(e.scale,e.pixelRows).scaleY},get axisScale(){return Se(e.scale,e.pixelRows)}})).views(e=>({get deletionDrawing(){return e.graph?He(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 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ep(e){return Q(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function gt(e){return e.flatMap(t=>Q(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function ht({views:e,connectedViewId:t,assemblyName:n}){let o=gt(e).filter(a=>ep(a)).filter(a=>a.assemblyNames.includes(n));return o.find(a=>a.id===t)??(o.length===1?o[0]:void 0)}function ft(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function ls(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var tp=1e3;function Go(e,t=tp){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 gs(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 hs({session:e,location:t,assembly:n,connectedViewId:o,tracks:r=[]}){let a=ht({views:e.views,connectedViewId:o,assemblyName:n}),i;return a?(ls(e,`Could not show ${n} ${qe(t)}`,Promise.resolve(a.navToLocString(_t(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${qe(t)}`,init:{assembly:n,loc:_t(t),tracks:r}}).id,i}function fs({session:e,location:t,assembly:n,connectedViewId:o}){let r=ht({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 ms(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=>ft(e,r)):[]}function bs({session:e,contributors:t,trackId:n,graphTrackId:o}){let r=ms(e,o),a=ms(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:_t(d),...o!==void 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r=en(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return va(gs(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&ht({views:[...(0,ve.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?Ue(n):void 0,r=o?Ke(e.assemblyResolver,o):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,c=a&&i&&s?we({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:Go(o),assembly:r}:void 0,reference:a&&d?{location:Go(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,ve.getContainingView)(e)}catch{return}return Ji(t)?t:void 0}}));var ys=ws.views(e=>({get walkStripShown(){return Xr({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:Ge(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Vt(t,{width:e.paneWidth})},get cutsWholeWalks(){return zr(_(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?Yr(e.graph,[t.reference,...t.rows],o):[]},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Ot(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=Ke(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){o++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...Cn(a.axis,a.bp)}})}return{reads:n.slice(0,ro),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-ro)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let r=o.haplotype===void 0?void 0:`${o.sample}#${o.haplotype}`,a=t===0?e.graphRegion?.assemblyName:Ke(e.assemblyResolver,{sample:o.sample,haplotype:r});return{label:o.label,assembly:a,location:{sample:o.sample,haplotype:r,refName:o.axis.contig,...Cn(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?Hr([t.reference,...t.rows],n):void 0}}));var ks=ys.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&_(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?pt(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?la(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?ca(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?xa(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?pa(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?fa(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;return e.showReferenceStrip&&e.referenceStripApplies&&t?ka(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}):[]},get referenceStripFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?pt(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}=Sa(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=>Dr(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:Ot(e.nodePositions?.[o],t)}:void 0},referenceStripNodeAt(t,n){let o=e.referenceStripFrame;return e.referenceStripShown&&o?Ra(e.referenceStripBlocks,o,t,n):void 0},get paperCss(){return Li(e.darkMode?Kt:Ut)},get referenceStripZonePx(){return e.referenceStripShown?ya:0}}));function np(e,t,n){if(!(!e||!t))return Wr(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var Rs=ks.views(e=>({get paneCeiling(){return Math.max(Yt,e.paneHeight??Mi)},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=e.host?this.canvasHeight:this.paneCeiling,o=(e.walkRowGroups?.sections.length??0)*Lr;return jr(t.rows.length+1,n-this.fitPadTopBase-F-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?Ar(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return np(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=Ye(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?nt(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:$r(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=wa(e.tubeMapGenes);return F+Math.max(0,t-1)*ba+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=l=>(e.paneWidth-this.fitPadLeft-l)/t.w,s=l=>e.pixelRows?t.h+l+F<=a?1/0:0:(a-l-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(vi/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?It(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?At({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(Yt,r.total);let a=Math.max(Yt,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?Ie(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):Ie(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 Zn(rt(e),Bi)},applyHighlights(t){let{litNode:n,hoveredEdge:o,selectedNode:r}=e,a=new Map;r!==null&&a.set(r,Ci),n!==null&&n!==r&&a.set(n,oo),t.setNodeHighlights(a),t.setEdgeHighlight(e.chosenHighlightOnHover?o:null,oo)},paint(t){let n=Zr();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?Kt:Ut)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:i}=e;if(!o||!r||!a||!i)return;ge(e.viewportDirty,e.positionsVersion);let s=(0,Po.untracked)(()=>e.viewportToBuild());return{batch:Bt({...it(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,Po.untracked)(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:s,referenceRamp:e.referenceRamp,version:e.positionsVersion}),viewportBounds:s}},get overlayLabels(){return sa(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?ra(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}-${t.end}`,a=Ee(e.sourceGfaLocation),i=n?.type==="GbzBaseSyntenyAdapter"?Ee(n.gbzDbLocation):void 0,s=a?{gfa:a,region:r}:i&&t&&r?{gbz:{db:i,index:Ee(n.haplotypeIndexLocation),region:r,haplotypes:e.cutHaplotypes?.map(p=>o?.[p]??p),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!s)return;let c=e.showGenes?e.geneTrack:void 0,d=c?(0,Ss.getSession)(e).tracks.find(p=>p.trackId===c.trackId):void 0,l=d?(0,rn.expandTabixShorthand)((0,rn.readConfObject)(d,"adapter"),"gffGzLocation"):void 0,b=l?.type==="Gff3TabixAdapter"?{file:Ee(l.gffGzLocation),index:Ee(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...s,genes:b?.file&&b.index?b:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...lo({quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.colorDomain}),walks:e.walkLayers.length?e.walkLayers.map(p=>p.color?p:p.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${_(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 ${_(e.chosenLayoutMode).label} layout`},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?mo(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?go(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?da(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?pt(o,r):void 0;return t&&n&&a?ua(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&&ga(r.yScale)?o.mismatches.filter(i=>ha(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?ho(o,r,t,n):null)??ma(e.tubeMapConnectors,e.connectorZoneBottom,t,n)??null}}));function xs(e,t,n){let o=Math.min(48,t,n);return Math.max(0,o-(e+t))-Math.max(0,e-(n-o))}function Ms(e,t,n){return{translateX:t.translateX+xs(e.minX*t.scaleX+t.translateX,e.w*t.scaleX,n.width),translateY:t.translateY+xs(e.minY*t.scaleY+t.translateY,e.h*t.scaleY,n.height)}}function Ls(e,t,n){let o=e.minX*t.scaleX+t.translateX,r=e.minY*t.scaleY+t.translateY;return o<n.width&&o+e.w*t.scaleX>0&&r<n.height&&r+e.h*t.scaleY>0}var vs=Rs.actions(e=>({keepDrawingInView(){let t=e.layoutBounds,n=e.viewBox;if(!t||e.viewportOwner==="fit"||!e.paneMeasured||n.width<=0||n.height<=0)return;let o=Ms(t,e,n);e.viewportOwner!=="host"&&(e.translateX=o.translateX),e.translateY=o.translateY}})).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},setHighlightOnHover(t){e.highlightOnHover=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let o=We(n,t);at.inherit(n,o),e.graph=o}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setShowReferenceStrip(t){e.showReferenceStrip=t},setTubeMapFold(t){e.tubeMapFold=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setWalkLayers(t){e.walkLayers=t},liftWalks(t){let n=new Map(e.walkLayers.map(o=>[o.walk,o]));e.walkLayers=t.map(o=>n.get(o)??{walk:o})},setFacet(t){t!==e.facet.field&&(e.facet.domain=[]),e.facet.field=t},setFacetColumns(t){e.facet.columns=t},toggleWalk(t){let 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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,Us.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!O(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var fp=(0,Js.defineLaunchKeys)()({});function Do(e){e.addViewType(()=>new qs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Fo(),launchKeys:fp,ReactComponent:(0,Ks.lazy)(()=>import("./chunks/GraphGenomeView-VIKLXNQD.js"))}))}var Zs=b(q(),1),Fe=b(be(),1),$o=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function bp(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"),...$o.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Vo(e){e.addTrackType(()=>{let 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t.cutSubgraph(t.adapterConfig,n,{hops:r?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:r?"coarse":void 0,...O(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let o=t.tierAt(n.bpPerPx);return t.coarseCut=o==="coarse",t.cutRegion=wo(n,t.capFor(o),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let o=O(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||lc(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&os(t.cutRegion,n,o)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,C.isAlive)(t)&&mc(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let o=O(t.chosenLayoutMode);t.setLayoutMode(n);let r=O(n),a=t.host?Qt(t.host):void 0;return 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Lc(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Mc(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Mc(`${t}.links.bed.gz`,n,o)}:e}function Yo(e){let{coarse:t,baseUri:n}=e;return Lc(typeof t=="object"&&t!==null?{...e,coarse:Lc({baseUri:n,...t})}:e)}var gn=(e,t)=>(0,hn.ConfigurationSchema)(e,{indexType:{model:vc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),kp=(0,hn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Sp=(0,hn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:gn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:gn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:kp},{explicitlyTyped:!0,preProcessSnapshot:Yo}),Tc=Sp;function Uo(e){e.addAdapterType(()=>new Gc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Yo,configSchema:Tc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-GYRNCGT2.js").then(t=>t.default)}))}var xp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Rp(e){return sr(e).toLowerCase().endsWith(".gbz.db")}function Mp(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 Lp(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Rp(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&cr(e))return dr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Ko(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Mp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>Lp(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>xp.has(n)?"GraphTrack":t(n,o))}var Ic=b(ie(),1),fn=b(Yc(),1),qo=b(zc(),1),Cc=b(Uc(),1);function Pc(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 vp(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function Ac(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Tp(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 Nc(e,t,n){let o=[],r=ht(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 Tp(i)){let c=Pc(s.hoverHighlight);c&&Ac(c,n)&&o.push({key:typeof s.id=="string"?s.id:"graph-track",region:c})}if(Q(i)&&i.type==="GraphGenomeView"&&vp(i,t,a)){let s=Pc(i.hoverHighlight);s&&Ac(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var $e=b(de(),1),Gp=(0,Cc.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,fn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,fn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Pp=(0,qo.observer)(function({model:t,region:n}){let{classes:o}=Gp(),r=t.getHighlightCoords(n);return r?(0,$e.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),Ap=(0,qo.observer)(function({model:t}){let{views:n}=(0,Ic.getSession)(t);return(0,$e.jsx)($e.Fragment,{children:Nc([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,$e.jsx)(Pp,{model:t,region:r},`graph-hover-${o}`))})}),Ec=Ap;var Bc=b(de(),1),Np="LinearGenomeView-TracksContainerComponent";function Jo(e){e.contributeToExtensionPoint(Np,({model:t})=>(0,Bc.jsx)(Ec,{model:t},"graphgenomeview-hover-highlight"))}var Fc=b(be(),1);function Ip(e){return e.views(t=>({get adapterConfig(){return we(t,t.parentTrack.configuration)}}))}function Zo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Fc.DisplayType&&$o.includes(t.name)&&t.extendStateModel(Ip),t))}var Dc="GraphGenomeView";var $c="6.3.1";var Qo=class extends Vc.default{constructor(){super(...arguments);this.name=Dc;this.version=$c}install(n){Do(n),Wo(n),Vo(n),Oo(n),Jo(n),Uo(n),zo(n),_n(n),Wn(n),Ko(n),Zo(n),n.addRpcMethod(()=>new et(n)),n.addRpcMethod(()=>new Qe(n)),n.addRpcMethod(()=>new Ze(n))}configure(n){try{(0,Oc.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};
+`);return[{type:"radio",label:"Every sample",checked:n===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:o(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:n!==void 0&&!o(t),onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Ti,{model:e,onClose:r}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return[{type:"radio",label:"None",checked:t===void 0,onClick:()=>{e.setWalkRowGroupBy(void 0)}},...e.walkRowGroupFields.map(n=>({type:"radio",label:n,checked:t===n,onClick:()=>{e.setWalkRowGroupBy({field:n})}}))]},layoutOptionMenuItems(){return[...Ce.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:Ni.map(({bp:t,label:n})=>({type:"radio",label:n,checked:e.tubeMapFold===t,disabled:t>0&&e.graph?.reads!==void 0,onClick:()=>{e.setTubeMapFold(t),e.recomputeLayout()}}))}]:[],...e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:[{type:"radio",label:"Whole window",checked:e.repeatKey==="",onClick:()=>{e.setRepeatKey("")}},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({type:"radio",label:`${n} \xB7 ${o.toLocaleString()} bp unit`,checked:e.repeatKey===t,onClick:()=>{e.setRepeatKey(t)}}))]}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){return[{type:"checkbox",label:"Show bubble halos",checked:e.showBubbles,onClick:()=>{e.setShowBubbles(!e.showBubbles)}},{type:"checkbox",label:"Show deletion edges",checked:e.showDeletionEdges,onClick:()=>{e.toggleDeletionEdges()}},{type:"checkbox",label:"Show hover highlight",checked:e.chosenHighlightOnHover,onClick:()=>{e.setHighlightOnHover(!e.chosenHighlightOnHover)}},{type:"checkbox",label:"Show genes on the backbone",checked:e.showGenes,onClick:()=>{e.setShowGenes(!e.showGenes)}},...e.referenceStripApplies?[{type:"checkbox",label:"Show reference strip",checked:e.showReferenceStrip,onClick:()=>{e.setShowReferenceStrip(!e.showReferenceStrip)}}]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:ri,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&Vs(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}},{label:"Copy figure spec",icon:Qa,disabled:e.figureSpecUnavailable!==void 0,disabledHelpText:e.figureSpecUnavailable,onClick:()=>{let t=e.figureSpec(),n=(0,he.getSession)(e);navigator.clipboard.writeText(`${JSON.stringify(t,null,2)}
+`).then(()=>{n.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(o=>{n.notify(`Could not copy the figure spec: ${String(o)}`)})}}]},highlightMenuItems(){let t=e.walkChoices;if(t.length===0||!e.liftsWalks)return[];let n=r=>e.walkLayers.some(a=>a.walk===r),o=t.length>Ai;return[{type:"subHeader",label:"Highlight"},...o?[{label:"Choose haplotypes...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Gi,{model:e,onClose:r}])}}]:[],...(o?t.filter(r=>n(r.name)):t).map(r=>({type:"checkbox",label:r.label,checked:n(r.name),onClick:()=>{e.toggleWalk(r.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{(0,he.getSession)(e).queueDialog(r=>[Pi,{model:e,onClose:r}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...kr.map(({value:r,label:a})=>({type:"radio",label:r==="walk"?"A panel per haplotype":a,checked:e.facet.field===r,onClick:()=>{e.setFacet(r)}}))]:[]]},colorSchemeLabel(t){let n=Gn.find(o=>o.value===t)?.label??t;return t==="auto"?`${n} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:n},graphMenuItems(){let t=this.layoutOptionMenuItems();return[{label:`Layout: ${_(e.chosenLayoutMode).label.replace(/ layout$/,"")}`,icon:ti,subMenu:[...wr.map(n=>({type:"radio",label:n.label,checked:e.chosenLayoutMode===n.value,disabled:e.graph?!n.available(e.graph):!1,onClick:()=>{e.switchLayout(n.value)}})),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.zoomToFit()}}]]},{label:`Color: ${this.colorSchemeLabel(e.chosenColorScheme)}`,icon:oi,subMenu:Gn.map(n=>({type:"radio",label:this.colorSchemeLabel(n.value),checked:e.chosenColorScheme===n.value,onClick:()=>{e.setColorScheme(n.value)}}))},{label:"Show...",icon:ii,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let n of Ta({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:o=>{e.showInLinearView(o)},onShowSynteny:o=>{e.showSyntenyView(o)}}))(0,Os.pushLaunchViewMenuItem)(t,n);return t}}));function dn(){return _s}var Io=f(K(),1);function $s(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function Co(e){let t=(0,Io.readConfObject)(e,"assemblyNames"),n=$s(t)?t.slice(1):[];return n.length>0?n:void 0}function pn(e){let t=(0,Io.readConfObject)(e,"assemblyNames");return $s(t)?t[0]:void 0}function un(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function lp(e){return("uri"in e?e.uri.split(/[?#]/)[0]:"localPath"in e?e.localPath:"name"in e?e.name:"").split(/[\\/]/).at(-1)??""}function Eo(){return z.types.compose("GraphGenomeView",Hs.BaseViewModel,dn(),z.types.model({type:z.types.literal("GraphGenomeView"),gfaLocation:z.types.maybe(z.types.frozen()),loadedRegion:z.types.maybe(z.types.frozen()),loadedTrackId:z.types.optional(z.types.string,""),subgraphContext:z.types.optional(z.types.number,1),subgraphHaplotypes:z.types.maybe(z.types.frozen()),maxRegionBp:z.types.optional(z.types.number,ot)})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(n){t(n),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,Ws.getSession)(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(lp(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let o=e.sourceTrack,r=n.end-n.start,a=o?un(pn(o),n.assemblyName):void 0;if(!o)e.setError(new Error(`The track this graph was cut from, "${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 (${xe(r)}) \u2014 zoom in to view graph (max ${xe(e.maxRegionBp)})`));else return e.cutSubgraph(be(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,z.addDisposer)(e,(0,js.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!_(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var gp=(0,Ys.defineLaunchKeys)()({});function Bo(e){e.addViewType(()=>new zs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Eo(),launchKeys:gp,ReactComponent:(0,Xs.lazy)(()=>import("./chunks/GraphGenomeView-ULQ6U5MK.js"))}))}var Us=f(K(),1),Be=f(fe(),1),Fo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function hp(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"),...Fo.map(r=>o(n(r)))].filter(r=>r!==void 0)}function Do(e){e.addTrackType(()=>{let t=(0,Us.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Be.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Be.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Be.createBaseTrackModel)(e,"GraphTrack",t)});for(let o of hp(e))n.addDisplayType(o);return n})}function Vo(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...o}=t;return n.addView("GraphGenomeView",o),t})}var wc=f(Oe(),1),yc=f(qs(),1);var Qs=f(K(),1),ec=f(Zs(),1),Oo=f(ne(),1);function tc(){return(0,Qs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Oo.types.enumeration("LayoutMode",vt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Oo.types.enumeration("ColorScheme",Tt),defaultValue:"auto"},highlightOnHover:{type:"boolean",defaultValue:!0},...(0,ec.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var mc=f(Oe(),1);var Fe=f(K(),1),lc=f(fe(),1),gc=f(oc(),1),hc=f(cr(),1),_o=f(ae(),1),fc=f(ac(),1),I=f(ne(),1),mn=f(sc(),1);var cc=f(ce(),1),dc=(0,te.createSvgIcon)((0,cc.jsx)("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var wt=f(St(),1);function pc(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 uc(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 fp=(0,mc.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-O6IYVHNJ.js"));function bc(e){return I.types.compose("LinearGraphDisplay",lc.BaseDisplay,(0,fc.default)(),dn(),I.types.model({type:I.types.literal("LinearGraphDisplay"),configuration:(0,Fe.ConfigurationReference)(e),pane:I.types.maybe(I.types.frozen()),overviewRowsChoice:I.types.maybe(I.types.frozen()),overviewRowOrder:I.types.maybe(I.types.frozen()),cutRegion:I.types.maybe(I.types.frozen()),coarseCut:I.types.optional(I.types.boolean,!1),maxRegionBp:I.types.optional(I.types.number,ot),subgraphContext:I.types.optional(I.types.number,1),subgraphHaplotypes:I.types.maybe(I.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 be(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,Fe.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,Fe.getConf)(t,"colorScheme")},get defaultHighlightOnHover(){return(0,Fe.getConf)(t,"highlightOnHover")},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 (${xe(n.end-n.start)}, max ${xe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return(0,gc.computeSvgReady)({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return(0,mn.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,mn.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=un(pn(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,..._(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let o=t.tierAt(n.bpPerPx);return t.coarseCut=o==="coarse",t.cutRegion=fo(n,t.capFor(o),_(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let o=_(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||uc(t.dense,n)||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Qi(t.cutRegion,n,o)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,I.isAlive)(t)&&pc(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let o=_(t.chosenLayoutMode);t.setLayoutMode(n);let r=_(n),a=t.host?Zt(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,I.addDisposer)(t,(0,wt.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,I.addDisposer)(t,(0,wt.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,I.addDisposer)(t,(0,wt.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,I.addDisposer)(t,(0,wt.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:o}=t,r=n&&o?Zt(o):void 0;r&&t.settleOn(r)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Zt(t.host):void 0,o=t.sourceTrackId;if(!n||!o||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let r=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:o,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:r,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-r),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,I.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,_o.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({cutMenuItems(){if(t.adapterConfig.type!=="GbzBaseSyntenyAdapter")return[];let n=Co(t.parentTrack.configuration),o=t.subgraphHaplotypes,r=a=>{t.setSubgraphHaplotypes(a),t.cut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:"Every haplotype in the 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,_o.getSession)(t).queueDialog(n=>[fp,{model:t,open:!0,onClose:n}])},async renderSvg(n){let{renderGraphTrackSvg:o}=await import("./chunks/renderSvg-J7L374ND.js");return o(t,n)},trackMenuItems(){let n=t.launchMenuItems();(0,hc.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Ht,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let o=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...o.length>0?[{label:"Haplotypes",icon:dc,subMenu:o}]:[],...t.graphMenuItems(),{label:"Settings",icon:Ga,onClick:()=>{this.openSettings()}},...n]}}))}function $o(e){e.addDisplayType(()=>{let t=tc();return Object.assign(new yc.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:bc(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,wc.lazy)(()=>import("./chunks/LinearGraphDisplay-KM5SOSQQ.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Rc=f(Wt(),1);var Ho=f(K(),1),kc=f(ne(),1);function Wo(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:o?"CSI":"TBI",location:{uri:`${t}.${o?"csi":"tbi"}`,baseUri:n}}}:e}var bp=(0,Ho.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,Ho.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:kc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Wo}),Sc=bp;function jo(e){e.addAdapterType(()=>new Rc.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:Wo,configSchema:Sc,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CAXB5FGR.js").then(t=>t.default)}))}var Tc=f(Wt(),1);var gn=f(K(),1),Lc=f(ne(),1);function xc(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Mc(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:xc(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:xc(`${t}.links.bed.gz`,n,o)}:e}function Xo(e){let{coarse:t,baseUri:n}=e;return Mc(typeof t=="object"&&t!==null?{...e,coarse:Mc({baseUri:n,...t})}:e)}var ln=(e,t)=>(0,gn.ConfigurationSchema)(e,{indexType:{model:Lc.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),wp=(0,gn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ln("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:ln("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),yp=(0,gn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:ln("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:ln("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:wp},{explicitlyTyped:!0,preProcessSnapshot:Xo}),vc=yp;function zo(e){e.addAdapterType(()=>new Tc.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Xo,configSchema:vc,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-GYRNCGT2.js").then(t=>t.default)}))}var kp=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Sp(e){return ar(e).toLowerCase().endsWith(".gbz.db")}function Rp(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 xp(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Sp(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 Yo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Rp),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,o,r)=>xp(n,o,r)??t(n,o,r)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,o)=>kp.has(n)?"GraphTrack":t(n,o))}var Nc=f(ae(),1),hn=f(zc(),1),Uo=f(Xc(),1),Ic=f(Yc(),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 Pc(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 Ac(e,t,n){let o=[],r=gt(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&&Pc(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&&Pc(s,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return o}var De=f(ce(),1),vp=(0,Ic.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,hn.alpha)(e.palette.primary.main,.08),borderLeft:`1px solid ${(0,hn.alpha)(e.palette.primary.main,.4)}`,borderRight:`1px solid ${(0,hn.alpha)(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Tp=(0,Uo.observer)(function({model:t,region:n}){let{classes:o}=vp(),r=t.getHighlightCoords(n);return r?(0,De.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),Gp=(0,Uo.observer)(function({model:t}){let{views:n}=(0,Nc.getSession)(t);return(0,De.jsx)(De.Fragment,{children:Ac([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,De.jsx)(Tp,{model:t,region:r},`graph-hover-${o}`))})}),Cc=Gp;var Ec=f(ce(),1),Pp="LinearGenomeView-TracksContainerComponent";function Ko(e){e.contributeToExtensionPoint(Pp,({model:t})=>(0,Ec.jsx)(Cc,{model:t},"graphgenomeview-hover-highlight"))}var Bc=f(fe(),1);function Ap(e){return e.views(t=>({get adapterConfig(){return be(t,t.parentTrack.configuration)}}))}function qo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof Bc.DisplayType&&Fo.includes(t.name)&&t.extendStateModel(Ap),t))}var Fc="GraphGenomeView";var Dc="6.4.0";var Jo=class extends Vc.default{constructor(){super(...arguments);this.name=Fc;this.version=Dc}install(n){Bo(n),$o(n),Do(n),Vo(n),Ko(n),zo(n),jo(n),_n(n),Hn(n),Yo(n),qo(n),n.addRpcMethod(()=>new Qe(n)),n.addRpcMethod(()=>new Ze(n)),n.addRpcMethod(()=>new Je(n))}configure(n){try{(0,Oc.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Ht,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{Jo as default};
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