jbrowse-plugin-graphgenomeviewer 7.4.3 → 7.5.0

package/dist/chunks/{renderSvg-7G6NWBXF.js → renderSvg-3PPAEMBT.js}

@@ -1,2 +1,2 @@
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${I})`,children:[e("g",{transform:`translate(0 ${x-2})`,children:V.draw(6)}),e("g",{transform:`translate(0 ${L})`,children:e(N,{model:t,lift:l,drawPaths:!1,width:c,height:d,rasterize:n})})]},_.name)})]})}function T({model:t,rasterize:n=!1,idPrefix:o}){let r=t.paneWidth,a=t.canvasHeight,i=!!t.layoutResult?.tubeMap,p={rasterizeLayers:n};return f("g",{"data-testid":"graph-pane-svg",children:[t.facetPanels?e(rt,{model:t,rasterize:n,idPrefix:o}):i?e(G,{width:r,height:a,opts:p,paint:c=>{z(J(c),t,{highlightNode:null})}}):e(N,{model:t,lift:t.drawnHighlight,drawPaths:t.effectiveDrawPaths,width:r,height:a,rasterize:n}),t.facetPanels?null:f(v,{children:[e(B,{model:t}),e(X,{model:t}),e(tt,{model:t}),e(H,{model:t}),e(F,{model:t,vector:!0}),e(et,{model:t})]}),t.referenceStripShown?e(G,{width:r,height:a,opts:p,paint:c=>{A(J(c),t,{lit:void 0,dpr:1})}}):null,t.facetPanels?null:e(Q,{model:t,idPrefix:o})]})}function nt({model:t,opts:n}){return e(T,{model:t,rasterize:!!n?.rasterizeLayers,idPrefix:`graph-${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 +1,7 @@
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wa=W("GbzBaseSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},gbzDbLocation:E("/path/to/graph.gbz.db"),haplotypeIndexLocation:E(""),readsLocation:E(""),readsIndex:$("GbzBaseReadsIndex"),samplesTsvLocation:E(""),subgraphSnarls:{type:"stringEnum",model:M.enumeration("SnarlOutput",["none","contained","overlapping"]),defaultValue:Oe.snarls},referenceSample:{type:"string",defaultValue:""},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},context:{type:"number",defaultValue:Oe.context,advanced:!0},nodeLimit:{type:"number",defaultValue:Oe.limit,advanced:!0}},{explicitlyTyped:!0,preProcessSnapshot:e=>{let{uri:t,baseUri:o,reads:r}=e;return{...e,...t?{gbzDbLocation:{uri:t,baseUri:o}}:{},...typeof r=="string"?{readsLocation:{uri:r,baseUri:o},...Ma(r,o)}:{}}}});function Ma(e,t){let{name:o,query:r}=Ao(e);return o.endsWith(".gz")?{readsIndex:{location:{uri:`${o}.tbi${r}`,baseUri:t}}}:{}}var cn=wa;function Vt(e){e.addAdapterType(()=>new 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it=Kn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ce(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Uo(o),n=R(e);return r===void 0?void 0:Xo(Be(n,r),Be(n,t.assemblyName))},cutChangedFrom(t){let o=zo(O(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function Jt(){return M.compose("GraphGenomeView",kn,it,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:xt($e),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:xt(Ge)})).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 sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 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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"),...Ut.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Xt(e){e.addTrackType(()=>{let t=W("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 ni(e))o.addDisplayType(r);return o})}function Kt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var st=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var qn=st&&st.__esModule?st.default:st;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 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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=ii("computeSvgReady");var cm=fe&&fe.__esModule?fe.default:fe;var pt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ta=pt&&pt.__esModule?pt.default:pt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],si=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=si("editPlotMenuItems");var mm=we&&we.__esModule?we.default:we;var Me=JBrowseExports["@jbrowse/render-core/displayPhase"],ra=e=>Me!=null&&e in Object(Me)?Me[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to 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M.compose("LinearGraphDisplay",dn,ta(),it,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:Q(t,"layoutMode"),color:Q(t,"color"),size:Q(t,"size"),layers:Q(t,"layers"),facet:Q(t,"facet"),rows:Q(t,"rows"),hover:Q(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&&Ce(o))??(r&&Rt(r))},get coarseAboveBpPerPx(){return ui(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=Zt*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 (${ce(o.end-o.start)}, max ${ce(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(Zt*(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),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=O(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||qt(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(()=>{j(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?Ke(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||O(o).cutMargins!==O(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 R(t).rpcManager.call(ie(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});j(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,I(()=>{let n=t.sourceAdapter;return n&&Jo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new 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0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Ke(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{...ci(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&&R(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Yo(o))return[];let n=Ce(o),a=Rt(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 ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){R(t).queueDialog(o=>[di,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-7G6NWBXF.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();at(o,{label:"Graph genome view",icon:et,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:an,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:sn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...oa(t)]}}))}function Qt(e){e.addDisplayType(()=>{let t=Qn();return Object.assign(new qn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ia(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:te(()=>import("./chunks/LinearGraphDisplay-O4SQSXJJ.js"))}),{adapterCapabilities:["getSubgraph"]})})}function mi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:ve(t,o,r)}:e}var li=W("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:$("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:mi}),sa=li;function eo(e){e.addAdapterType(()=>new oe({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED 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hi=W("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:$("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:$("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),yi=W("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:$("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:$("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:$("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:hi},{explicitlyTyped:!0,preProcessSnapshot:gi}),ca=yi;function to(e){e.addAdapterType(()=>new oe({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-55DGDID2.js").then(t=>t.default)}))}var bi=W("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:$("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:We}),ua=bi;function oo(e){e.addAdapterType(()=>new oe({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny 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r("RgfaTabixWalks")}}function ro(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Mi),e.addToExtensionPoint("Core-preProcessTrackConfig",ki),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Si(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>fi.has(o)?"GraphTrack":t(o,r))}function da(e){let t;if(J(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 xi(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 Ri(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>J(o)&&Array.isArray(o.displays)?o.displays.filter(r=>J(r)&&r.type==="LinearGraphDisplay"):[])}function la(e,t,o){let r=[],n=Je(e),a=new Set(n.map(i=>J(i)?i.id:void 0));for(let i of n){if(J(i)&&i.id===t)for(let s of Ri(i)){let p=da(s.hoverHighlight);p&&ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if(J(i)&&i.type==="GraphGenomeView"&&xi(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 Ti=nn()(e=>({highlight:{height:"100%",position:"absolute",background:_e(e.palette.primary.main,.08),borderLeft:`1px solid ${_e(e.palette.primary.main,.4)}`,borderRight:`1px solid ${_e(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Gi=ft(function({model:t,region:o}){let{classes:r}=Ti(),n=t.getHighlightCoords(o);return n?C("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Li=ft(function({model:t}){let{views:o}=R(t);return C(wo,{children:la([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>C(Gi,{model:t,region:n},`graph-hover-${r}`))})}),ga=Li;var vi="LinearGenomeView-TracksContainerComponent";function no(e){e.contributeToExtensionPoint(vi,({model:t})=>C(ga,{model:t},"graphgenomeview-hover-highlight"))}function Ai(e){return e.views(t=>({get adapterConfig(){return Kr(t,t.parentTrack.configuration)}}))}function ao(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof mn&&Ut.includes(t.name)&&t.extendStateModel(Ai),t))}var ha="GraphGenomeView";var ya="7.4.3";var io=class extends pn{constructor(){super(...arguments);this.name=ha;this.version=ya}install(o){Yt(o),Qt(o),Xt(o),Kt(o),no(o),to(o),eo(o),Vt(o),oo(o),Ft(o),ro(o),ao(o),o.addRpcMethod(()=>new Fe(o)),o.addRpcMethod(()=>new He(o)),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ee(o))}configure(o){try{yo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:et,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{io as default};
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strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:On,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&ma(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>Sr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{x(e).queueDialog(a=>[kr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{x(e).queueDialog(a=>[Mr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...ee(mr.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Bt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=Z(e.chosenLayoutMode),r=la.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${Kt(o)}${o.value==="force"?` (${r})`:""}`,icon:jn,subMenu:[...tr.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?la.map(([i,s])=>({...a,label:`${Kt(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:Kt(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:Wn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:ee(Bt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:lr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of fn({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)}}))dt(t,n);return t}}));var ut=ga.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ee(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&ar(o),n=x(e);return r===void 0?void 0:ir(Ne(n,r),Ne(n,t.assemblyName))},cutChangedFrom(t){return e.cutsWholeWalks!==e.cutsWholeWalksIn(t)||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 Zt(){return M.compose("GraphGenomeView",Vn,ut,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:Lt(Xe),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:Lt(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(ue(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 (${de(a)}) \u2014 zoom in to view graph (max ${de(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ue(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(At(n,r)):void 0):o(r&&At(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(ue(t)))},afterAttach(){e.graph||e.load(),L(e,B(()=>e.walkStrip,t=>{e.loadedTrackId&&e.cutsWholeWalks!==e.cutsWholeWalksIn(e.chosenLayoutMode,!t)&&e.load()}))}}))}var Mi=Hn()({});function Qt(e){e.addViewType(()=>new Fn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Zt(),launchKeys:Mi,ReactComponent:oe(()=>import("./chunks/GraphGenomeView-KI4FQ5A7.js"))}))}var eo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Si(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"),...eo.map(n=>r(o(n)))].filter(n=>n!==void 0)}function to(e){e.addTrackType(()=>{let t=j("GraphTrack",{},{baseConfiguration:Cn(e),explicitIdentifier:"trackId"}),o=new Bn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:In(e,"GraphTrack",t)});for(let r of Si(e))o.addDisplayType(r);return o})}function oo(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var ct=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var ha=ct&&ct.__esModule?ct.default:ct;var ye=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],xi=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}),ba=xi("trackHeightConfigSchemaFields"),wm=ye&&ye.__esModule?ye.default:ye;function ya(){return j("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",Xe),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",ve),defaultValue:"nodes"},...ba({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],Ri=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 fa=Ri("computeSvgReady");var Lm=fe&&fe.__esModule?fe.default:fe;var mt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var wa=mt&&mt.__esModule?mt.default:mt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],Ti=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}),ka=Ti("editPlotMenuItems");var Am=we&&we.__esModule?we.default:we;var ke=JBrowseExports["@jbrowse/render-core/displayPhase"],Ma=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}),Sa=Ma("computeActivityPhase");var xa=Ma("computeDisplayStatusPhase"),Cm=ke&&ke.__esModule?ke.default:ke;function ro(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 Gi=new Set(["scale","translateX","translateY"]);function Li(e){return Object.fromEntries(Object.keys(vr.properties).filter(t=>!Gi.has(t)).map(t=>[t,e[t]]))}var no=10;function vi(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/no:void 0}var Pi=oe(()=>import("./chunks/GraphTrackSettingsDialog-UQNMDXTE.js"));function Ra(e){return M.compose("LinearGraphDisplay",Pn,wa(),ut,M.model({type:M.literal("LinearGraphDisplay"),configuration:Fo(e),layoutEngine:or(Ko,"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: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&&Ee(o))??(r&&vt(r))},get coarseAboveBpPerPx(){return vi(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=no*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 (${de(o.end-o.start)}, max ${de(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return fa({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return xa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>Sa({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))Ho(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(no*(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=pn(o,t.capFor(r),Z(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=Z(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||ro(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&dn(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&&xt(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)||Z(o).cutMargins!==Z(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;L(t,()=>{o?.abort()}),L(t,B(()=>{let n=t.sourceAdapter;return n&&rr(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"})),L(t,B(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(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;L(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"})),L(t,B(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-Qe)?.total??0)+Qe;(t.facetGrid?.total??0)+Qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,B(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Te(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Te(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||ro(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...Li(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!nr(o))return[];let n=Ee(o),a=vt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=u=>{t.setSubgraphHaplotypes(u),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${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=>[Pi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-3PPAEMBT.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();dt(o,{label:"Graph genome view",icon:ot,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!xt(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:kn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:Mn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...ka(t)]}}))}function ao(e){e.addDisplayType(()=>{let t=ya();return Object.assign(new ha({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Ra(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-RPZUZSM2.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Ai(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Be(t,o,r)}:e}var Bi=j("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:_("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Ai}),Ta=Bi;function io(e){e.addAdapterType(()=>new Q({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:Ta,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-TJYI7KEN.js").then(t=>t.default)}))}function Ga(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Be(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Be(`${t}.links.bed.gz`,o,r)}:e}function Ci(e){let{coarse:t,baseUri:o,csi:r}=e;return xe(Ga(typeof t=="object"&&t!==null?{...e,coarse:Ga({baseUri:o,csi:r,...t})}:e))}var Ii=j("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Ei=j("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Ii},{explicitlyTyped:!0,preProcessSnapshot:Ci}),La=Ei;function so(e){e.addAdapterType(()=>new Q({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:La,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-5ZMJLFZP.js").then(t=>t.default)}))}var Ni=["LinearMultiSampleVariantDisplay"],Fi=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function Hi(e,t){return e?`Pinned to ${et(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function Vi(e,t){let o=x(e),r=t.flatMap(n=>n?[Rn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function ji(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return ie(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 Sn(this.adapterConfig.pinned)},get formsFloor(){return xn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=vo(t),r=sn(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=()=>{Vi(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:Hi(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&&et(n)===et(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Fi.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 po(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof nt&&Ni.includes(t.name)&&t.extendStateModel(ji),t))}var Wi=j("WalkFormsAdapter",{walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:Tn},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:xe}),va=Wi;function uo(e){e.addAdapterType(()=>new Q({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:va,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-CAJOWOEX.js").then(t=>t.default)}))}var Oi=j("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:xe}),Pa=Oi;function co(e){e.addAdapterType(()=>new Q({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:Pa,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-VI3KA2GX.js").then(t=>t.default)}))}var Di=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function _i(e){return ft(e).toLowerCase().endsWith(".gbz.db")}function zi(e){let t=e.adapter;return t?.type!==void 0&&un.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function $i(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Wo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ji(e,t,o){let r=n=>qo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&_i(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Xo(e))return r("RgfaTabixAdapter");if(ft(e).endsWith(jo)&&(t!==void 0||_o(e)))return r("RgfaTabixWalks")}}function mo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",zi),e.addToExtensionPoint("Core-preProcessTrackConfig",$i),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ji(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Di.has(o)?"GraphTrack":t(o,r))}function lo(e){let t;if(O(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 Yi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Aa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Ba(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>O(o)&&Array.isArray(o.displays)?o.displays.filter(r=>O(r)&&r.type==="LinearGraphDisplay"):[])}function Ca(e,t,o){let r=[],n=Re(e),a=new Set(n.map(i=>O(i)?i.id:void 0));for(let i of n){if(O(i)&&i.id===t)for(let s of Ba(i)){let p=lo(s.hoverHighlight);p&&Aa(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of O(i)?[...Ba(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((u,m)=>{let S=lo(u);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(O(i)&&i.type==="GraphGenomeView"&&Yi(i,t,a)){let s=lo(i.hoverHighlight);s&&Aa(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ui=wn()(e=>({highlight:{height:"100%",position:"absolute",background:Ye(e.palette.primary.main,.08),borderLeft:`1px solid ${Ye(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Ye(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Xi=St(function({model:t,region:o}){let{classes:r}=Ui(),n=t.getHighlightCoords(o);return n?I("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),qi=St(function({model:t}){let{views:o}=x(t);return I(Co,{children:Ca([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>I(Xi,{model:t,region:n},`graph-hover-${r}`))})}),Ia=qi;var Ki="LinearGenomeView-TracksContainerComponent";function go(e){e.contributeToExtensionPoint(Ki,({model:t})=>I(Ia,{model:t},"graphgenomeview-hover-highlight"))}function Zi(e){return e.views(t=>({get adapterConfig(){return cn(t,t.parentTrack.configuration)}}))}function ho(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof nt&&eo.includes(t.name)&&t.extendStateModel(Zi),t))}var Ea="GraphGenomeView";var Na="7.5.0";var bo=class extends Gn{constructor(){super(...arguments);this.name=Ea;this.version=Na}install(o){Qt(o),ao(o),to(o),oo(o),go(o),so(o),io(o),Wt(o),co(o),uo(o),po(o),Dt(o),mo(o),ho(o),o.addRpcMethod(()=>new De(o)),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o))}configure(o){try{Po(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:ot,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{bo as default};
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