jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.4

package/dist/chunks/{renderSvg-Z7YIXVQ5.js → renderSvg-ZIUOPWJQ.js}

@@ -1,2 +1,2 @@
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e(T,{model:t,rasterize:!!n?.rasterizeLayers,idPrefix:`graph-${t.id}`})}function Gt(t,n){return Y(t,n,nt)}export{Gt as renderGraphTrackSvg};
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w=JBrowseExports["@jbrowse/core/util/paintLayer"],Z=t=>w!=null&&t in Object(w)?w[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/core/util/paintLayer' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t}),G=Z("PaintLayer"),lt=w&&w.__esModule?w.default:w;var k={fontFamily:"sans-serif",fontSize:11},x=16,q=2,J=t=>t;function N({model:t,lift:n,drawPaths:o,width:r,height:a,rasterize:i}){let p=t.buildDrawing(n,o);if(!p)return null;let c=i?q:1,d=i?void 0:M(r,a),h=d?.canvas??document.createElement("canvas");d||(h.width=Math.round(r*c),h.height=Math.round(a*c));let{scaleX:u,scaleY:y,translateX:l,translateY:s}=t.screenTransform,g=new E(h);return 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e("g",{fontFamily:k.fontFamily,children:t.overlayLabels.sizes.map(({key:n,text:o,x:r,y:a,kind:i,leader:p})=>f("g",{children:[p?e("line",{x1:p.arcX,y1:p.arcY,x2:p.labelX,y2:p.labelY,stroke:"#18181c"}):null,e(K,{x:r,y:a,text:o,fontSize:10,anchor:"middle",bold:i==="deletion"})]},n))})}function et({model:t}){return e("g",{fontFamily:k.fontFamily,children:t.visibleRowLabels.map(({label:n,y:o,top:r})=>e(K,{x:10,y:r,text:n,fontSize:11,anchor:"start"},o))})}function rt({model:t,rasterize:n,idPrefix:o}){let r=t.facetPanels,a=t.facetGrid,i=t.facetPlacement;if(!r||!a||!i)return null;let{columns:p,width:c,height:d}=a,h=a.total+S+14,u=O(t).map((l,s)=>D(l,`${o}-facet-key-${s}`)),y=u.map((l,s)=>u.slice(0,s).reduce((g,b)=>g+b.width+14,6));return f(v,{children:[e("g",{transform:`translate(0 ${h})`,children:u.map((l,s)=>l.draw(y[s]))}),r.map((l,s)=>{let g=i.cells[s],b=g%p*(c+S),I=Math.floor(g/p)*(L+d+S),_=l.walks[0],V=D($(t,_),`${o}-facet-${s}`);return f("g",{transform:`translate(${b} 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e(T,{model:t,rasterize:!!n?.rasterizeLayers,idPrefix:`graph-${t.id}`})}function Gt(t,n){return Y(t,n,nt)}export{Gt as renderGraphTrackSvg};
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package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

@@ -1,7 +1,6 @@
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at=Kn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ae(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Uo(o),n=x(e);return r===void 0?void 0:Xo(Pe(n,r),Pe(n,t.assemblyName))},cutChangedFrom(t){let o=zo(F(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function $t(){return 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0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(ce(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${pe(a)}) \u2014 zoom in to view graph (max ${pe(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ce(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=x(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Tt(n,r)):void 0):o(r&&Tt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),H(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(ce(t)))},afterAttach(){e.graph||e.load(),G(e,C(()=>e.walkStrip,()=>{e.loadedTrackId&&!F(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var oi=Mn()({});function Jt(e){e.addViewType(()=>new fn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:$t(),launchKeys:oi,ReactComponent:ee(()=>import("./chunks/GraphGenomeView-UCOAMRF7.js"))}))}var Yt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function ri(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Yt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Ut(e){e.addTrackType(()=>{let t=j("GraphTrack",{},{baseConfiguration:hn(e),explicitIdentifier:"trackId"}),o=new gn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:yn(e,"GraphTrack",t)});for(let r of ri(e))o.addDisplayType(r);return o})}function Xt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var it=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var qn=it&&it.__esModule?it.default:it;var ye=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],ni=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Zn=ni("trackHeightConfigSchemaFields"),em=ye&&ye.__esModule?ye.default:ye;function Qn(){return j("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",ze),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Re),defaultValue:"nodes"},...Zn({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var be=JBrowseExports["@jbrowse/core/svg/svgReady"],ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ea=ai("computeSvgReady");var pm=be&&be.__esModule?be.default:be;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ta=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ii=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),oa=ii("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var fe=JBrowseExports["@jbrowse/render-core/displayPhase"],ra=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),na=ra("computeActivityPhase");var aa=ra("computeDisplayStatusPhase"),lm=fe&&fe.__esModule?fe.default:fe;function Kt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var si=new Set(["scale","translateX","translateY"]);function pi(e){return Object.fromEntries(Object.keys(yr.properties).filter(t=>!si.has(t)).map(t=>[t,e[t]]))}var qt=10;function ci(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/qt:void 0}var ui=ee(()=>import("./chunks/GraphTrackSettingsDialog-MR7X75EY.js"));function ia(e){return M.compose("LinearGraphDisplay",dn,ta(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:_o(Fo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&xt(r))},get coarseAboveBpPerPx(){return ci(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=qt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${pe(o.end-o.start)}, max ${pe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ea({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return aa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>na({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=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(qt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Yr(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Kt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Ur(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;G(t,()=>{o?.abort()}),G(t,C(()=>{let n=t.sourceAdapter;return n&&Jo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),G(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),G(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;G(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),G(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),G(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Kt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...pi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Yo(o))return[];let n=Ae(o),a=xt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=u=>{t.setSubgraphHaplotypes(u),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[ui,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-Z7YIXVQ5.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:an,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:sn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...oa(t)]}}))}function Zt(e){e.addDisplayType(()=>{let t=Qn();return Object.assign(new qn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ia(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-AJ5OZN27.js"))}),{adapterCapabilities:["getSubgraph"]})})}function di(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Ge(t,o,r)}:e}var mi=j("MinigraphBubbleAdapter",{bubblesLocation:N("/path/to/graph.bb.bed.gz"),index:_("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:di}),sa=mi;function Qt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:sa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-PEQK5NII.js").then(t=>t.default)}))}function pa(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Ge(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Ge(`${t}.links.bed.gz`,o,r)}:e}function li(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(pa(typeof t=="object"&&t!==null?{...e,coarse:pa({baseUri:o,csi:r,...t})}:e))}var gi=j("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:N("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),hi=j("RgfaTabixAdapter",{segmentsLocation:N("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:N(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:gi},{explicitlyTyped:!0,preProcessSnapshot:li}),ca=hi;function eo(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-Q63YLPK4.js").then(t=>t.default)}))}var yi=j("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:N("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:N(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),ua=yi;function to(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-N5PFI4LS.js").then(t=>t.default)}))}var bi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function wi(e){return lt(e).toLowerCase().endsWith(".gbz.db")}function fi(e){let t=e.adapter;return t?.type!==void 0&&Xr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Mi(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function ki(e,t,o){let r=n=>Ho({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&wi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Vo(e))return r("RgfaTabixAdapter");if(lt(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function oo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",fi),e.addToExtensionPoint("Core-preProcessTrackConfig",Mi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>ki(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>bi.has(o)?"GraphTrack":t(o,r))}function da(e){let t;if(z(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Si(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function xi(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>z(o)&&Array.isArray(o.displays)?o.displays.filter(r=>z(r)&&r.type==="LinearGraphDisplay"):[])}function la(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>z(i)?i.id:void 0));for(let i of n){if(z(i)&&i.id===t)for(let s of xi(i)){let p=da(s.hoverHighlight);p&&ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if(z(i)&&i.type==="GraphGenomeView"&&Si(i,t,a)){let s=da(i.hoverHighlight);s&&ma(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ri=nn()(e=>({highlight:{height:"100%",position:"absolute",background:De(e.palette.primary.main,.08),borderLeft:`1px solid ${De(e.palette.primary.main,.4)}`,borderRight:`1px solid ${De(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ti=bt(function({model:t,region:o}){let{classes:r}=Ri(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Gi=bt(function({model:t}){let{views:o}=x(t);return A(fo,{children:la([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ti,{model:t,region:n},`graph-hover-${r}`))})}),ga=Gi;var Li="LinearGenomeView-TracksContainerComponent";function ro(e){e.contributeToExtensionPoint(Li,({model:t})=>A(ga,{model:t},"graphgenomeview-hover-highlight"))}function vi(e){return e.views(t=>({get adapterConfig(){return Kr(t,t.parentTrack.configuration)}}))}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof mn&&Yt.includes(t.name)&&t.extendStateModel(vi),t))}var ha="GraphGenomeView";var ya="7.4.2";var ao=class extends pn{constructor(){super(...arguments);this.name=ha;this.version=ya}install(o){Jt(o),Zt(o),Ut(o),Xt(o),ro(o),eo(o),Qt(o),Et(o),to(o),Ht(o),oo(o),no(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{yo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{ao as default};
+`);return[{type:"radio",label:"Every sample",checked:o===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:r(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:o!==void 0&&!r(t),onClick:()=>{S(e).queueDialog(n=>[mr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return ee([{value:void 0,label:"None"},...e.walkRowGroupFields.map(o=>({value:o,label:o}))],t,o=>{e.setWalkRowGroupBy(o===void 0?void 0:{field:o})})},tubeMapPanelMenuItems(){let{graph:t,walkRowSampleTable:o}=e,{field:r}=e.facetSetting,n=r===""?e.walkRowGroupBy?.field:void 0,a=i=>!!t&&Ke(t,i).length>1;return[...ee(zr.map(i=>({value:i.field,label:i.label,disabled:i.field!==""&&!a({by:i.field})})),n?void 0:r,i=>{e.setFacet(i),i===""&&e.setWalkRowGroupBy(void 0)}),...ee(e.walkRowGroupFields.map(i=>({value:i,label:`By ${i}`,disabled:!o||!a({by:"column",field:i,table:o})})),n,i=>{e.setFacet(""),e.setWalkRowGroupBy({field:i})})]},layoutOptionMenuItems({repeat:t=!0}={}){return[...pe.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:ee(yr.map(({bp:o,label:r})=>({value:o,label:r,disabled:o>0&&e.graph?.reads!==void 0})),e.graph?.reads?0:e.tubeMapFold,e.setTubeMapFold)},{label:"Panels",subMenu:this.tubeMapPanelMenuItems()},{label:"Routes",subMenu:ee(wr,e.tubeMapRoutes,e.setTubeMapRoutes)},...e.walkRowGroupFields.length>0?[{label:"Tube color",subMenu:ee(["",...e.walkRowGroupFields].map(o=>({value:o,label:o?`By ${o}`:"By role"})),e.tubeMapColorBy,e.setTubeMapColorBy)}]:[]]:[],...t&&e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:ee(e.repeatOptions,e.selectedRepeat?.key??"",e.setRepeatKey)}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:ee(ve.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:In,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&oa(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>hr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{S(e).queueDialog(a=>[lr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{S(e).queueDialog(a=>[gr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...ee(ar.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=At.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=D(e.chosenLayoutMode),r=ra.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${Yt(o)}${o.value==="force"?` (${r})`:""}`,icon:Cn,subMenu:[...Yo.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?ra.map(([i,s])=>({...a,label:`${Yt(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:Yt(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:Bn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:ee(At.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:ir,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of dn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))st(t,n);return t}}));var pt=na.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ie(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Qo(o),n=S(e);return r===void 0?void 0:er(Ne(n,r),Ne(n,t.assemblyName))},cutChangedFrom(t){let o=Xo(D(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function Ut(){return f.compose("GraphGenomeView",Pn,pt,f.model({type:f.literal("GraphGenomeView"),gfaLocation:f.maybe(f.frozen()),loadedRegion:f.maybe(f.frozen()),loadedTrackId:f.optional(f.string,""),layoutMode:Tt(Je),color:f.maybe(f.frozen()),size:f.maybe(f.frozen()),layers:f.maybe(f.frozen()),facet:f.maybe(f.frozen()),rows:f.maybe(f.frozen()),hover:Tt(ve)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(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;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(de(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${ue(a)}) \u2014 zoom in to view graph (max ${ue(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===de(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=S(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(vt(n,r)):void 0):o(r&&vt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),W(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(de(t)))},afterAttach(){e.graph||e.load(),A(e,B(()=>e.walkStrip,()=>{e.loadedTrackId&&!D(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var mi=An()({});function Xt(e){e.addViewType(()=>new vn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Ut(),launchKeys:mi,ReactComponent:oe(()=>import("./chunks/GraphGenomeView-SEAPDRXS.js"))}))}var Kt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function li(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Kt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function qt(e){e.addTrackType(()=>{let t=H("GraphTrack",{},{baseConfiguration:Rn(e),explicitIdentifier:"trackId"}),o=new xn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:Tn(e,"GraphTrack",t)});for(let r of li(e))o.addDisplayType(r);return o})}function Zt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var ut=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var aa=ut&&ut.__esModule?ut.default:ut;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],gi=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),ia=gi("trackHeightConfigSchemaFields"),mm=be&&be.__esModule?be.default:be;function sa(){return H("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:f.enumeration("LayoutMode",Je),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:f.enumeration("HoverHighlight",ve),defaultValue:"nodes"},...ia({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],hi=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var pa=hi("computeSvgReady");var km=fe&&fe.__esModule?fe.default:fe;var dt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ua=dt&&dt.__esModule?dt.default:dt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],yi=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),da=yi("editPlotMenuItems");var xm=we&&we.__esModule?we.default:we;var ke=JBrowseExports["@jbrowse/render-core/displayPhase"],ca=e=>ke!=null&&e in Object(ke)?ke[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),ma=ca("computeActivityPhase");var la=ca("computeDisplayStatusPhase"),Tm=ke&&ke.__esModule?ke.default:ke;function Qt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var bi=new Set(["scale","translateX","translateY"]);function fi(e){return Object.fromEntries(Object.keys(Mr.properties).filter(t=>!bi.has(t)).map(t=>[t,e[t]]))}var eo=10;function wi(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/eo:void 0}var ki=oe(()=>import("./chunks/GraphTrackSettingsDialog-EVIIGC5G.js"));function ga(e){return f.compose("LinearGraphDisplay",Mn,ua(),pt,f.model({type:f.literal("LinearGraphDisplay"),configuration:vo(e),layoutEngine:Uo(_o,"stress"),cutRegion:f.maybe(f.frozen()),coarseCut:f.optional(f.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:te(t,"layoutMode"),color:te(t,"color"),size:te(t,"size"),layers:te(t,"layers"),facet:te(t,"facet"),rows:te(t,"rows"),hover:te(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ie(o))??(r&&Lt(r))},get coarseAboveBpPerPx(){return wi(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=eo*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${ue(o.end-o.start)}, max ${ue(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return pa({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return la({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>ma({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=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ao(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(eo*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Qr(o,t.capFor(r),D(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=D(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Qt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&en(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{W(t)&&t.recuts===a&&Mt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Te(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||D(o).cutMargins!==D(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await S(t).rpcManager.call(ie(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});W(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;A(t,()=>{o?.abort()}),A(t,B(()=>{let n=t.sourceAdapter;return n&&qo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),A(t,B(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),A(t,B(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;A(t,B(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),A(t,B(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-Ze)?.total??0)+Ze;(t.facetGrid?.total??0)+Ze>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),A(t,B(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Te(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Te(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Qt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...fi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&S(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Zo(o))return[];let n=Ie(o),a=Lt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=d=>{t.setSubgraphHaplotypes(d),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){S(t).queueDialog(o=>[ki,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-ZIUOPWJQ.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();st(o,{label:"Graph genome view",icon:tt,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!Mt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:mn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:ln,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...da(t)]}}))}function to(e){e.addDisplayType(()=>{let t=sa();return Object.assign(new aa({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ga(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-ZC4BQ27J.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Mi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Pe(t,o,r)}:e}var Si=H("MinigraphBubbleAdapter",{bubblesLocation:N("/path/to/graph.bb.bed.gz"),index:O("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Mi}),ha=Si;function oo(e){e.addAdapterType(()=>new Q({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:ha,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-3QM4XV47.js").then(t=>t.default)}))}function ya(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Pe(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Pe(`${t}.links.bed.gz`,o,r)}:e}function xi(e){let{coarse:t,baseUri:o,csi:r}=e;return Re(ya(typeof t=="object"&&t!==null?{...e,coarse:ya({baseUri:o,csi:r,...t})}:e))}var Ri=H("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:N("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:O("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.tier.links.bed.gz"),linksIndex:O("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Ti=H("RgfaTabixAdapter",{segmentsLocation:N("/path/to/graph.segs.bed.gz"),segmentsIndex:O("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.links.bed.gz"),linksIndex:O("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:N(""),walksIndex:O("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Ri},{explicitlyTyped:!0,preProcessSnapshot:xi}),ba=Ti;function ro(e){e.addAdapterType(()=>new Q({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ba,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-XSOIEWBK.js").then(t=>t.default)}))}var Li=["LinearMultiSampleVariantDisplay"],Gi=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function vi(e,t){return e?`Pinned to ${Qe(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function Ai(e,t){let o=S(e),r=t.flatMap(n=>n?[yn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function Pi(e){return e.props({formsPinned:f.maybe(f.frozen()),formsFloorBp:f.maybe(f.frozen())}).views(t=>({get configuredAdapter(){return Z(t.parentTrack.configuration,"adapter")},get walkForms(){return this.configuredAdapter.type==="WalkFormsAdapter"}})).views(t=>({get adapterConfig(){let o=t.configuredAdapter;return t.walkForms?{...o,...t.formsPinned?{pinned:t.formsPinned}:{},...t.formsFloorBp===void 0?{}:{floorBp:t.formsFloorBp}}:o},get formsWindow(){return gn(this.adapterConfig.pinned)},get formsFloor(){return hn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=ko(t),r=Zr(o)?Te(o):void 0;return r&&r.end>r.start?{refName:r.refName,start:Math.max(0,Math.floor(r.start)),end:Math.ceil(r.end)}:void 0}})).volatile(()=>({warnedWindow:void 0})).actions(t=>{let{setSources:o}=t,r=()=>{Ai(t,[t.warnedWindow,t.formsWindow])};return{setFormsPinned(n){r(),t.formsPinned=n},setFormsFloorBp(n){r(),t.formsFloorBp=n},setSources(n,a){t.walkForms&&(r(),t.warnedWindow=t.formsWindow),o?.(n,a)}}}).views(t=>{let{trackMenuItems:o}=t;return{formsMenuItems(){let r=t.formsWindow,n=t.visibleWindow;return[{label:vi(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the forms from the region the view shows. Panning and zooming leave the forms alone",disabled:!n||r!==void 0&&Qe(n)===Qe(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Gi.map(({label:a,value:i})=>({label:a,type:"radio",checked:t.formsFloor===i,onClick:()=>{t.setFormsFloorBp(i)}}))}]},trackMenuItems(){return t.walkForms?[...o(),...this.formsMenuItems()]:o()}}})}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Li.includes(t.name)&&t.extendStateModel(Pi),t))}var Ci=H("WalkFormsAdapter",{walksLocation:N("/path/to/graph.walks.bed.gz"),walksIndex:O("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:bn},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:Re}),fa=Ci;function ao(e){e.addAdapterType(()=>new Q({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:fa,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-FT2SW4H6.js").then(t=>t.default)}))}var Bi=H("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:N("/path/to/graph.walks.bed.gz"),walksIndex:O("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:N(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Re}),wa=Bi;function io(e){e.addAdapterType(()=>new Q({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:wa,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-3WRVNDLB.js").then(t=>t.default)}))}var Ii=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Ni(e){return yt(e).toLowerCase().endsWith(".gbz.db")}function Fi(e){let t=e.adapter;return t?.type!==void 0&&tn.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ei(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Bo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Vi(e,t,o){let r=n=>Do({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Ni(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Oo(e))return r("RgfaTabixAdapter");if(yt(e).endsWith(Co)&&(t!==void 0||Fo(e)))return r("RgfaTabixWalks")}}function so(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Fi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ei),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Vi(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Ii.has(o)?"GraphTrack":t(o,r))}function ka(e){let t;if($(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Hi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function ji(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>$(o)&&Array.isArray(o.displays)?o.displays.filter(r=>$(r)&&r.type==="LinearGraphDisplay"):[])}function Sa(e,t,o){let r=[],n=Ye(e),a=new Set(n.map(i=>$(i)?i.id:void 0));for(let i of n){if($(i)&&i.id===t)for(let s of ji(i)){let p=ka(s.hoverHighlight);p&&Ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if($(i)&&i.type==="GraphGenomeView"&&Hi(i,t,a)){let s=ka(i.hoverHighlight);s&&Ma(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Wi=cn()(e=>({highlight:{height:"100%",position:"absolute",background:ze(e.palette.primary.main,.08),borderLeft:`1px solid ${ze(e.palette.primary.main,.4)}`,borderRight:`1px solid ${ze(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Oi=kt(function({model:t,region:o}){let{classes:r}=Wi(),n=t.getHighlightCoords(o);return n?I("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Di=kt(function({model:t}){let{views:o}=S(t);return I(Ro,{children:Sa([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>I(Oi,{model:t,region:n},`graph-hover-${r}`))})}),xa=Di;var _i="LinearGenomeView-TracksContainerComponent";function po(e){e.contributeToExtensionPoint(_i,({model:t})=>I(xa,{model:t},"graphgenomeview-hover-highlight"))}function zi(e){return e.views(t=>({get adapterConfig(){return on(t,t.parentTrack.configuration)}}))}function uo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Kt.includes(t.name)&&t.extendStateModel(zi),t))}var Ra="GraphGenomeView";var Ta="7.4.4";var co=class extends fn{constructor(){super(...arguments);this.name=Ra;this.version=Ta}install(o){Xt(o),to(o),qt(o),Zt(o),po(o),ro(o),oo(o),Ht(o),io(o),ao(o),no(o),Wt(o),so(o),uo(o),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o)),o.addRpcMethod(()=>new He(o)),o.addRpcMethod(()=>new Ve(o))}configure(o){try{Mo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:tt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{co as default};
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