jbrowse-plugin-graphgenomeviewer 7.1.3 → 7.1.4

package/dist/chunks/{GraphGenomeView-LX7GDEDM.js → GraphGenomeView-PSDUS64B.js}

@@ -1,4 +1,4 @@
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+import{a as C}from"./chunk-NP42Y2MV.js";import"./chunk-BUY2PV7D.js";import"./chunk-RP3L3Z5W.js";import"./chunk-HM57SCYO.js";import{k as d}from"./chunk-VJ3SO4CH.js";import"./chunk-LELA7BG7.js";import"./chunk-VQUMZEGN.js";import"./chunk-WAMBI7OX.js";import"./chunk-W6EQLQ6H.js";import"./chunk-5O6YRJHL.js";import"./chunk-N6PQZSAX.js";import"./chunk-TUKJRVBS.js";import"./chunk-FVK2THE4.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-ZMOMFU2B.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as x}from"./chunk-YU7T5WOQ.js";import{A as l,F as L,H as p,e as s,j as v,o as n,x as G}from"./chunk-UGCNPRKC.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,S=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),T=i(function({model:e}){let{classes:t}=S(),[m,M]=x("");function u(){let o=m.trim();o&&e.loadGFAFromLocation({uri:o,locationType:"UriLocation"})}function N(o){let c=o.target.files?.[0];o.target.value="",c&&c.text().then(f=>e.loadGFA(f,c.name)).catch(f=>{e.setError(f)})}return r(l,{className:t.paper,children:[a("div",{className:t.header,children:a(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",a("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:o=>{N(o)}})]}),a(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[a(L,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{M(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),a(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),a("div",{className:t.footer,children:a(n,{size:"small",onClick:()=>{e.loadGFA(F,"Example graph")},children:"Load 4-node example"})}),e.error?a(s,{error:e.error}):null]})}),P=T;var A=i(function({model:e}){return e.hasGraph?a(C,{model:e}):e.canRetryLoad&&(e.error||e.loadCanceled)?a(g,{model:e}):r(y,{children:[e.isLoading?a(g,{model:e}):null,a("div",{hidden:e.isLoading,children:a(P,{model:e})})]})}),J=A;export{J as default};
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package/dist/chunks/{HighlightColorDialog-UK5VDDV6.js → HighlightColorDialog-2MP3C5AK.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{LinearGraphDisplay-QLPIRKPR.js → LinearGraphDisplay-FTFJFNKT.js}

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package/dist/chunks/chunk-HM57SCYO.js

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e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":ct(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?Vt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>Vt(pt(t,xe(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(xe(t)),s=new Set(n.nodes.filter(a=>o.has(a.name)).map(a=>a.id)),r=new Set;return n.edges.forEach((a,i)=>{s.has(a.from)&&s.has(a.to)&&r.add(i)}),{walks:[],nodeIds:s,edgeIndexes:r,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>Et(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,s=this.openBubbleFocus;return o?!n.some(r=>o.nodeIds.has(r)):!!s&&!this.bubbleIsOpen(t)&&!n.every(r=>s.nodeIds.has(r))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(It));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(It(o))&&n.add(It(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Io(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?ts(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?q(t,"trackId"):void 0},get sessionTracks(){let t=ne(e);return t.tracks.map(n=>({trackId:n.trackId,name:q(n,"name"),adapterType:q(n,"adapter").type,assemblies:Dn(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Fn(ne(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>mt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>no.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Us(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return zt(e.geneTrackChoices,e.geneTrackId)},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?.walkRowRuns;return t?cn(t):e.graph?Ie(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=ne(e),o=n.has(t)?n.get(t):void 0,s=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(a=>s[a]??[])]}},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=Js(t,e.geneTrack?.trackId);return n.length?new Ys({filters:n,jexl:po(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Qs(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,s=e.drawsLoadedReference||n!==void 0&&rn(t,[n])!==void 0;return t&&o&&s?sn(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?pe(e.drawnGraph):void 0},get nodeInk(){return xt(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?we(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?mc(n,t,t.unit):Ie(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[s,...r]=Nr([o.reference,...o.rows],t?.calls);return{...o,reference:s,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&&fo(t)?t:void 0},get walkRowGroupFields(){return nr(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=dr(t,n),s=(e.graph?.paths??[]).map(r=>W(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:ir(s.map(o)),unvalued:s.some(r=>o(r)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows;return t&&Qe(t.rows,e.walkRowSamples)},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?rr(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get drawsNodes(){return Q(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Je(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?rt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){Je(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:Yn(e.graph,e.bubbles,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return qe(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?ye(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,s=!1,r=!1;if(t&&e.drawnGraph)for(let a of e.drawnGraph.nodes)o&&!o[a.id]||(t.midpoints.has(a.id)?a.stable&&a.stable.rank>0&&(s=!0):r=!0);return{offReference:s,unplaced:r}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?Zn(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&&(!yt(n.length)||n.some(s=>s.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],s=this.tubeColorKind,r=e.tubeMapColoring;return s==="value"&&r?cr(o,t.referencePath,r.valueOf,r.palette):s==="tinted"?kn(o,t.referencePath,ar):s==="role"?kn(o,t.referencePath):n},fadeUnhovered(t,n,o){let s=new Set(e.hoveredRowWalks);return s.size>0?t.map((r,a)=>{let i=n[a]?.name??"";return s.has(i)||o!==void 0&&W(i).name===o?r:St}):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 ia(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&&aa(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&pe(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&yt(t.length)&&!t.some(o=>o.members)?We(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?ia(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 da=ca.views(e=>({get host(){let t=e.containingView;return As(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?de(t):[];return t?Rs(t,{maxGap:n.length>0?tn(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=ne(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,a])=>[a,r])),s=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>s(o.get(r))??s(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(mt.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let s=zt(o,"");return s?[[n,s]]:[]}))}})).views(e=>({get launchableAssemblies(){return vs(Ns(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&ot({views:[...ne(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?xs(n):void 0,s=o?nt(e.assemblyResolver,o):void 0,r=e.graphRegion,a=r?e.nodeSpan(t):void 0,i=r&&a?{sample:r.assemblyName,haplotype:void 0,refName:r.refName,...a}:void 0;return{own:o&&s?{location:Wn(o),assembly:s}:void 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t?er(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t?Zo(t):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap;return t?.coarse?Qo(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?kr(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=vr(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}),o=e.walkLift?void 0:e.openBubbleFocus;return o?n.map(s=>o.nodeIds.has(s.node)?s:{...s,colors:[St],faded:!0}):n}})).views(e=>({get 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