jbrowse-plugin-graphgenomeviewer 8.3.2 → 8.3.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "8.3.2",
+  "version": "8.3.3",
   "description": "JBrowse 2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -40,7 +40,7 @@
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
     "@eslint/js": "^10.0.1",
-    "@jbrowse/bandage-core": "^12.2.0",
+    "@jbrowse/bandage-core": "^12.2.1",
     "@jbrowse/cli": "^4.3.0",
     "@jbrowse/mobx-state-tree": "^6.10.0",
     "@jbrowse/plugin-linear-genome-view": "5.0.0-beta.18",

package/src/RgfaTabixAdapter/configSchema.ts

@@ -52,7 +52,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'RgfaTabixAdapter',
- *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5s.GRCh38',
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  *   defaultHaplotypes: ['HG002', 'HG00733', 'HG02257', 'NA19240'],
  * }

package/src/WalkFormsAdapter/configSchema.ts

@@ -34,7 +34,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'WalkFormsAdapter',
- *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5s.GRCh38',
  *   pinned: { refName: 'chr1', start: 109680000, end: 109715000 },
  *   exclude: ['CHM13'],
  * }

package/src/WalkTabixSyntenyAdapter/configSchema.ts

@@ -32,7 +32,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'WalkTabixSyntenyAdapter',
- *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5s.GRCh38',
  *   assemblyNames: ['hg38'],
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  * }

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.3.2'
+export const version = '8.3.3'

package/dist/chunks/chunk-D7MOOK6H.js

@@ -1,4 +0,0 @@
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e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get legendAtRest(){return e.hoveredNode===null&&e.hoveredRowWalks.length===0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return lo(e)},get paintSuperseded(){return!this.geometryPainted},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!this.geometryPainted)},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Yt(e.chosenLayoutMode,e.graph):!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?Se(t):[]},get effectiveDrawPaths(){return e.drawPaths&&Ve(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){let t=e.openBubbles.at(-1);return t&&!t.offReference&&t.end>t.start?{start:t.start,end:t.end}:e.statedColorDomain??e.graphRegion},get drawnReferenceRamp(){let t=e.drawnGraph;return t?Pe(t,this.rampDomain):void 0},get walkRamp(){return e.walkLayers.some(t=>t.color?.field==="reference")?this.drawnReferenceRamp:void 0},get modeDrawsNodes(){return j(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&&!e.walkCut&&n.length>0&&!e.layoutResult?.tubeMap?it(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facetSetting.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?ct(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!so.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Xe(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(no))},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":Oe(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?bt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>bt(He(t,de(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(de(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>tt(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(nt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(nt(o))&&n.add(nt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Dn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?rr(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=Y(e);return t.tracks.map(n=>({trackId:n.trackId,name:Cn(n,t),adapterType:je(n).type,assemblies:Jt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Kt(Y(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>pt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Ko.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Jo(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return lt(e.geneTrackChoices,e.geneTrackId)},get walkRowAnnotation(){return mt(this.geneTrack)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?Nn(e.graph):void 0},get cutWalkRows(){let t=e.walkCut,n=t?.walkRowRuns,o=this.rowVisitsNeeded;return t&&n&&o&&e.graphRegion?Dr(t,e.graphRegion,void 0,!0):n?Pt(n):e.graph?ue(e.graph,e.graphRegion,void 0,{visits:o}):void 0},get rowVisitsNeeded(){return e.chosenLayoutMode==="walkrows"&&(e.walkRibbons||e.layerSet.has("walkBlocks")||e.walkRowOrder==="shared")},assemblySpellings(t){let{assemblyManager:n}=Y(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(s=>r[s]??[])]}},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=e.containingView;if(!t)return;let n=qo(t,e.geneTrack?.trackId);return n.length?new Or({filters:n,jexl:xn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Zo(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,r=e.drawsLoadedReference||n!==void 0&&Pn(t,[n])!==void 0;return t&&o&&r?An(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?Q(e.drawnGraph):void 0},get nodeInk(){return qe(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get depthRange(){let t=e.graph?.nodes;if(!t?.length)return;let n=1/0,o=-1/0;for(let{depth:r}of t)n=Math.min(n,r),o=Math.max(o,r);return{min:n,max:o,mean:Zn(e.graph)}},get busiestLink(){return e.graph?Qn(e.graph):0},get allDeletions(){return e.graph&&this.drawsNodes?Fe(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=e.rowVisitsNeeded,r=t?n?Dr(n,t,t.unit,o):ue(e.graph,t,t.unit,{visits:o}):e.cutWalkRows;if(!r)return;let[a,...s]=Qo([r.reference,...r.rows],t?.calls);return{...r,reference:a,rows:s}},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&&Tn(t)?t:void 0},get walkRowGroupFields(){return So(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=To(t,n),r=(e.graph?.paths??[]).map(a=>ce(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Po(r.map(o)),unvalued:r.some(a=>o(a)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&ve(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return hn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Mo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowRibbons(){let t=this.walkRowBars;if(!e.walkRibbons||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return fn(n,we(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return gn(n,we(n))},get drawsNodes(){return j(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ce(e.graph,n,t):[]},get bubbleHalos(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:an(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return Je(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?De(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return e.drawsNodes||!!e.layoutResult?.tubeMap},get referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!T(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?wn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!Ve(n.length)||n.some(r=>r.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],r=this.tubeColorKind,a=e.tubeMapColoring;return r==="value"&&a?Ao(o,t.referencePath,a.valueOf,a.palette):r==="tinted"?Ft(o,t.referencePath,Lo):r==="role"?Ft(o,t.referencePath):n},fadeUnhovered(t,n,o){let r=new Set(e.hoveredRowWalks);return r.size>0?t.map((a,s)=>{let i=n[s]?.name??"";return r.has(i)||o!==void 0&&ce(i).name===o?a:Ze}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return jr(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&Xr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&Q(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&Ve(t.length)&&!t.some(o=>o.members)?Se(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?jr(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var zr=Yr.views(e=>({get host(){let t=e.containingView;return tr(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?J(t):[];return t?wr(t,{maxGap:n.length>0?vt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Y(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([a,s])=>[s,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 e.sessionTracks)if(pt.has(n.adapterType)&&mt(n)===e.walkRowAnnotation)for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let r=lt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return br(Rr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get 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n&&e.graph&&e.chosenHover!=="off"?fr(e.graph,n,e.assemblyResolver,e.graphRegion?.assemblyName):[]}}));var Ur=zr.views(e=>({get walkStripShown(){return Zt({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:ve(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ie(t,{width:e.paneWidth})},cutsWholeWalksIn(t,n=e.walkStrip){let o=j(t);return e.sourceAdapter?.type==="GbzBaseSyntenyAdapter"&&Qt(o,{walkStrip:n&&o.drawsNodes,host:!!e.host})},get cutsWholeWalks(){return this.cutsWholeWalksIn(e.chosenLayoutMode)},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?en(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:me(e.assemblyResolver,o),span:{refName:n.contig,...ot(n,t.bp)}}},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:dt(e.nodePositions?.[t],e.toScreen)}})).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{assembly:s,span:i}=e.rowLocation(a,a.axis),c=s?e.geneTracksByAssembly.get(s):void 0;if(!s||!c){o++;continue}n.push({row:a.name,trackId:c.trackId,region:{assemblyName:s,...i}})}return{reads:n.slice(0,_t),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-_t)}}},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{sample:r,haplotype:a,assembly:s,span:i}=e.rowLocation(o,o.axis);return{label:o.label,assembly:t===0?e.graphRegion?.assemblyName:s,location:{sample:r,haplotype:a,...i}}},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?bo([t.reference,...t.rows],n):void 0}}));var Kr=Ur.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&j(e.drawnLayoutMode??e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostBpFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?or(t,n):void 0}})).views(e=>({get hostFrame(){return e.hostPlacesX?e.hostBpFrame:void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?Ro(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t?yo(t):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap;return t?.coarse?ko(t,t.coarse.deviations):[]},get tubeMapConnectedBoxes(){let t=this.tubeMapReference,{layoutResult:n}=e;return t&&!n?.referenceAxis&&!n?.tubeMapPanels?[...t.values()].flat():void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes&&!e.layoutResult?.tubeMapPanels?Do(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;if(!e.showReferenceStrip||!e.referenceStripApplies||!t)return[];let n=Yo(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}),o=e.walkLift?void 0:e.openBubbleFocus;return o?n.map(r=>o.nodeIds.has(r.node)?r:{...r,colors:[Ze],faded:!0}):n}})).views(e=>({get 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n&&o&&o.w>0?ze({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-Zr)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=st+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-hs?t+2*st:ms},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(et,o.total+Zr);let r=Math.max(et,e.legendSize.height+2*st+e.referenceStripZonePx),a=this.fitPads,s=a.top+a.bottom;if(e.pixelRows)return Math.min(n,Math.max(r,t.h+s));let i=e.paneWidth-a.left-a.right;return t.w>0&&i>0?Math.min(n,Math.max(r,t.h*Math.max(i/t.w,this.minFitScale)+s)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:z,top:z,right:z,bottom:z}:{left:this.fitPadLeft,top:this.fitPadTop,right:X,bottom:X}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,r=this.fitPads;return t?Ne(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:r.left,padTop:r.top,padRight:r.right,padBottom:r.bottom}):void 0}})).views(e=>({viewportToBuild(){return Yn(mo(e),co)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,io]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=er();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:ro)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:s}=e;if(!o||!r||!a||!s)return;Ae(e.viewportDirty,e.positionsVersion);let i=At(()=>e.viewportToBuild()),c=Qe({...Be(a,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:r,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,edgeWidth:e.linkWidth,highlight:t,axis:At(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===a&&qr(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return _o(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Fo(t,o.id,o.length)??"not on this 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0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,rowAnnotation:e.walkRowAnnotation,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps}}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var kn=$(F("path",{d:"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z"}),"LineStyle");var Qr=$(F("path",{d:"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z"}),"CompareArrows");var ea=$(F("path",{d:"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2"}),"HighlightAlt");var gs="Linear genome view",ws="Linear synteny view",bs="No synteny track in this session aligns these assemblies";function ta({label:e,icon:t,entries:n,entryLabel:o,onSelect:r,disabledHelpText:a,nameTheOnlyEntry:s=!0}){let[i]=n,c=a?[{label:e,icon:t,disabled:!0,disabledHelpText:a,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:s?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:r(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(d=>({label:o(d),onClick:r(d)}))}]}function Xg({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:r}){let a=n[0]?.coverage??e.length;return[...ta({label:gs,icon:kn,entries:t,entryLabel:s=>`${s.sample} ${oe(s)}`,onSelect:s=>()=>{o({location:s,assembly:s.sample})}}),...e.length>=2?ta({label:`${ws} (${a} assemblies)`,icon:Qr,entries:n,entryLabel:s=>s.coverage<a?`${s.name} (${s.coverage} of ${a})`:s.name,nameTheOnlyEntry:!1,disabledHelpText:bs,onSelect:s=>()=>{r(s.trackId)}}):[]]}function jg({own:e,reference:t,highlight:n,onShowLinear:o,onHighlight:r}){let a=[e?{label:`Open in ${e.assembly} \u2014 ${oe(e.location)}`,target:e}:void 0,t&&t.assembly!==e?.assembly?{label:`Open in ${t.assembly} \u2014 around this node`,target:t}:void 0].filter(s=>s!==void 0);return[...r&&n?[{label:`Highlight in ${n.assembly}`,icon:ea,onClick:()=>{r(n)}}]:[],...a.map(({label:s,target:i})=>({label:s,icon:kn,onClick:()=>{o(i)}}))]}var Kg=$(F("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 Qg=$(F("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 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H,la as I,rr as J,rh as K,ih as L,ph as M,ms as N,us as O,Zr as P,Ag as Q,kn as R,Xg as S,jg as T,Kg as U,Qg as V};
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