jbrowse-plugin-graphgenomeviewer 8.6.0 → 8.7.0

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Files changed (7) hide show
  1. package/dist/jbrowse-plugin-graphgenomeviewer.esm.js +4 -4
  2. package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map +3 -3
  3. package/package.json +2 -1
  4. package/src/WalkFormsAdapter/formsMenu.ts +18 -5
  5. package/src/WalkFormsAdapter/formsMenuHost.test.ts +61 -0
  6. package/src/index.ts +4 -1
  7. package/src/version.ts +1 -1
package/dist/jbrowse-plugin-graphgenomeviewer.esm.js CHANGED
@@ -1,9 +1,9 @@
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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}),Sa=Bi("trackHeightConfigSchemaFields"),Cm=be&&be.__esModule?be.default:be;var ye=JBrowseExports["@jbrowse/display-kit/facetConfigSchema"],Ii=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/facetConfigSchema' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),xa=Ii("facetConfigSchema");var Im=ye&&ye.__esModule?ye.default:ye;var Ra=V("GraphFacet",{columns:{type:"maybeNumber",description:"panels per row of a node layout's grid; unset fits them"}},{baseConfiguration:xa,retired:{domain:e=>({sort:e})}});function Ta(){return 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mt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var La=mt&&mt.__esModule?mt.default:mt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],Fi=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}),va=Fi("editPlotMenuItems");var Xm=we&&we.__esModule?we.default:we;var ke=JBrowseExports["@jbrowse/render-core/displayPhase"],Aa=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}),Pa=Aa("computeActivityPhase"),Ca=Aa("computeDisplayPhase");var Km=ke&&ke.__esModule?ke.default:ke;function io(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 Ni=new Set(["scale","translateX","translateY"]);function Hi(e){return Object.fromEntries(Object.keys(Br.properties).filter(t=>!Ni.has(t)).map(t=>[t,e[t]]))}var so=10;function Vi(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/so:void 0}var ji=oe(()=>import("./chunks/GraphTrackSettingsDialog-R3XOY32L.js"));function Ba(e){return M.compose("LinearGraphDisplay",In,La(),ct,M.model({type:M.literal("LinearGraphDisplay"),configuration:Vo(e),layoutEngine:ar(er,"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"),encoding:Q(t,"encoding"),size:Q(t,"size"),layers:Q(t,"layers"),facet:{field:Q(t,["facet","field"]),sort:Q(t,["facet","sort"]),columns:Q(t,["facet","columns"])},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&&Ee(o))??(r&&Pt(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=so*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 Ga({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return Ca({renderError:t.renderError,regionTooLarge:t.regionTooLarge,error:t.error},()=>Pa({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},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Wo(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(so*(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=mn(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||io(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&ln(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&&Tt(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?Ge(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});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;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&ir(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new 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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=>[ji,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-GF64RZ6B.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();dt(o,{label:"Graph genome view",icon:ot,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!Tt(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:Rn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:Tn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...va(t)]}}))}function po(e){e.addDisplayType(()=>{let t=Ta();return Object.assign(new Ma({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Ba(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-RRAXTQFC.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Wi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:xe(t,o,r)}:e}var Oi=V("MinigraphBubbleAdapter",{bubblesLocation:B("/path/to/graph.bb.bed.gz"),index:W("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Wi}),Ia=Oi;function co(e){e.addAdapterType(()=>new ee({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:Ia,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-2YTXBZYS.js").then(t=>t.default)}))}function Ea(e){let{uri:t,baseUri:o,csi:r,format:n}=e;return typeof t!="string"?e:n===2?{...e,graphLocation:{uri:`${t}${wt}`,baseUri:o},graphIndex:xe(`${t}${wt}`,o,r)}:{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:xe(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:xe(`${t}.links.bed.gz`,o,r)}}function Di(e){let{coarse:t,baseUri:o,csi:r}=e;return Re(Ea(typeof t=="object"&&t!==null?{...e,coarse:Ea({baseUri:o,csi:r,...t})}:e))}var _i=V("RgfaTabixCoarseTier",{uri:{type:"maybeString"},format:{type:"maybeNumber"},aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:B("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:W("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.tier.links.bed.gz"),linksIndex:W("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:W("RgfaCoarseGraphIndex")}),zi=V("RgfaTabixAdapter",{segmentsLocation:B("/path/to/graph.segs.bed.gz"),segmentsIndex:W("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.links.bed.gz"),linksIndex:W("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:W("RgfaGraphIndex"),walksLocation:B(""),walksIndex:W("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:_i},{explicitlyTyped:!0,preProcessSnapshot:Di}),Fa=zi;function uo(e){e.addAdapterType(()=>new ee({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Fa,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-RCGS6YVM.js").then(t=>t.default)}))}var $i=["LinearMultiSampleVariantDisplay"],Ji=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function Yi(e,t){return e?`Pinned to ${et(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function Ui(e,t){let o=x(e),r=t.flatMap(n=>n?[vn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function Xi(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return jo(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 Ln(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=Co(t),r=un(o)?Ge(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=()=>{Ui(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:Yi(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the 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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:Ji.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 mo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof nt&&$i.includes(t.name)&&t.extendStateModel(Xi),t))}var qi=V("WalkFormsAdapter",{walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:W("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:An},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:Re}),Na=qi;function lo(e){e.addAdapterType(()=>new ee({name:"WalkFormsAdapter",displayName:"Walk-file structural forms 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Qi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Zi(e){return kt(e).toLowerCase().endsWith(".gbz.db")}function es(e){let t=e.adapter;return t?.type!==void 0&&gn.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function ts(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Do(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function os(e,t,o){let r=n=>Zo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Zi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Qo(e))return r("RgfaTabixAdapter");if(kt(e).endsWith(Oo)&&(t!==void 0||$o(e)))return r("RgfaTabixWalks")}}function ho(e){e.addToExtensionPoint("Core-preProcessTrackConfig",es),e.addToExtensionPoint("Core-preProcessTrackConfig",ts),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>os(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Qi.has(o)?"GraphTrack":t(o,r))}function bo(e){let t;if(I(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 rs(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Va(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function ja(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>I(o)&&Array.isArray(o.displays)?o.displays.filter(r=>I(r)&&r.type==="LinearGraphDisplay"):[])}function Wa(e,t,o){let r=[],n=Te(e),a=new Set(n.map(i=>I(i)?i.id:void 0));for(let i of n){if(I(i)&&i.id===t)for(let s of ja(i)){let p=bo(s.hoverHighlight);p&&Va(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of I(i)?[...ja(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((c,m)=>{let S=bo(c);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(I(i)&&i.type==="GraphGenomeView"&&rs(i,t,a)){let s=bo(i.hoverHighlight);s&&Va(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var ns=xn()(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 ${Ye(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),as=Rt(function({model:t,region:o}){let{classes:r}=ns(),n=t.getHighlightCoords(o);return n?N("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),is=Rt(function({model:t}){let{views:o}=x(t);return N(Eo,{children:Wa([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>N(as,{model:t,region:n},`graph-hover-${r}`))})}),Oa=is;var ss="LinearGenomeView-TracksContainerComponent";function yo(e){e.contributeToExtensionPoint(ss,({model:t})=>N(Oa,{model:t},"graphgenomeview-hover-highlight"))}function ps(e){return e.views(t=>({get adapterConfig(){return hn(t,t.parentTrack.configuration)}}))}function fo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof nt&&ro.includes(t.name)&&t.extendStateModel(ps),t))}var Da="GraphGenomeView";var _a="8.6.0";var wo=class extends Pn{constructor(){super(...arguments);this.name=Da;this.version=_a}install(o){oo(o),po(o),no(o),ao(o),yo(o),uo(o),co(o),Dt(o),go(o),lo(o),mo(o),zt(o),ho(o),fo(o),o.addRpcMethod(()=>new De(o)),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o))}configure(o){try{Bo(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{wo as default};
8
+ `);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:()=>{x(e).queueDialog(n=>[xr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return te([{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&&Qe(t,i).length>1;return[...te(on.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)}),...te(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[...se.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:te(Lr.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:te(Pr,e.tubeMapRoutes,e.setTubeMapRoutes)},...e.walkRowGroupFields.length>0?[{label:"Tube color",subMenu:te(["",...e.walkRowGroupFields].map(o=>({value:o,label:o?`By ${o}`:"By role"})),e.tubeMapColorBy,e.setTubeMapColorBy)}]:[]]:[],...t&&e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:te(e.repeatOptions,e.selectedRepeat?.key??"",e.setRepeatKey)}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()},{type:"checkbox",label:"Ribbons between rows",checked:e.walkRibbons,onClick:()=>{e.setLayer("walkRibbons",!e.walkRibbons)}},{type:"checkbox",label:"Letter shared blocks",checked:e.layerSet.has("walkBlocks"),onClick:()=>{e.setLayer("walkBlocks",!e.layerSet.has("walkBlocks"))}},{type:"checkbox",label:"Order rows by shared sequence",checked:e.walkRowOrder==="shared",onClick:()=>{e.setWalkRowOrder(e.walkRowOrder==="shared"?void 0:"shared")}}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:te(Ae.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:$n,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&ba(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>Gr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{x(e).queueDialog(a=>[Rr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{x(e).queueDialog(a=>[Tr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...te(br.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=It.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=Z(e.chosenLayoutMode),r=ya.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${Zt(o)}${o.value==="force"?` (${r})`:""}`,icon:_n,subMenu:[...nr.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?ya.map(([i,s])=>({...a,label:`${Zt(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:Zt(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:zn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:te(It.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show",icon:yr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of Sn({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 ct=fa.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Fe(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&pr(o),n=x(e);return r===void 0?void 0:cr(Ee(n,r),Ee(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.walkRowSamples?.length?{expandSamples:e.walkRowSamples}:{}}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));var wa={scale:["scale","type"],domain:["scale","domain"],range:["scale","range"],labels:["scale","names"],scheme:["scale","scheme"],reverse:["scale","reverse"],domainMin:["scale","domainMin"],domainMax:["scale","domainMax"],domainMid:["scale","domainMid"],domainQuantile:["scale","domainQuantile"],unknown:["scale","unknown"],title:["legend","title"],descending:["legend","descending"]};function Ci(e){return Object.entries(e).some(([t,o])=>t in wa&&!(t==="scale"&&I(o)))}function eo(e){if(typeof e=="string")return{value:e};if(!I(e)||!Ci(e))return e;let t={},o={scale:{},legend:{}};for(let[r,n]of Object.entries(e)){let a=wa[r];!a||r==="scale"&&I(n)?t[r]=n:n!==void 0&&(o[a[0]][a[1]]=r==="scale"&&n==="categorical"?"ordinal":n)}for(let r of["scale","legend"])if(Object.keys(o[r]).length>0){let n=t[r];t[r]={...o[r],...I(n)?n:{}}}return t}var ka={color:e=>({encoding:{color:eo(e)}})};function to(){return M.compose("GraphGenomeView",Dn,ct,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:At(qe),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:At(Ae)})).preProcessSnapshot(e=>e.color===void 0?e:{...e,color:eo(e.color)}).views(e=>({get grammar(){return{layoutMode:e.layoutMode,encoding:{color:e.color},size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar({encoding:t,...o}){Object.assign(e,t?{...o,color:t.color}:o)}})).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 (${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===de(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(Bt(n,r)):void 0):o(r&&Bt(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),j(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(de(t)))},afterAttach(){e.graph||e.load(),L(e,C(()=>e.walkStrip,t=>{e.loadedTrackId&&e.cutsWholeWalks!==e.cutsWholeWalksIn(e.chosenLayoutMode,!t)&&e.load()}))}}))}var Bi=On()({});function oo(e){e.addViewType(()=>new Wn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:to(),launchKeys:Bi,ReactComponent:oe(()=>import("./chunks/GraphGenomeView-RD2XGX6D.js"))}))}var ro=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Ii(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"),...ro.map(n=>r(o(n)))].filter(n=>n!==void 0)}function no(e){e.addTrackType(()=>{let t=V("GraphTrack",{},{baseConfiguration:Nn(e),explicitIdentifier:"trackId"}),o=new En({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:Hn(e,"GraphTrack",t)});for(let r of Ii(e))o.addDisplayType(r);return o})}function ao(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 Ma=ut&&ut.__esModule?ut.default:ut;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],Fi=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}),Sa=Fi("trackHeightConfigSchemaFields"),Bm=be&&be.__esModule?be.default:be;var ye=JBrowseExports["@jbrowse/display-kit/facetConfigSchema"],Ei=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/facetConfigSchema' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),xa=Ei("facetConfigSchema");var Fm=ye&&ye.__esModule?ye.default:ye;var Ra=V("GraphFacet",{columns:{type:"maybeNumber",description:"panels per row of a node layout's grid; unset fits them"}},{baseConfiguration:xa,retired:{domain:e=>({sort:e})}});function Ta(){return V("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",qe),defaultValue:"auto"},encoding:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:Ra,rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Ae),defaultValue:"nodes"},...Sa({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId",retired:ka})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],Ni=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 Ga=Ni("computeSvgReady");var Ym=fe&&fe.__esModule?fe.default:fe;var mt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var La=mt&&mt.__esModule?mt.default:mt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],Hi=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}),va=Hi("editPlotMenuItems");var qm=we&&we.__esModule?we.default:we;var ke=JBrowseExports["@jbrowse/render-core/displayPhase"],Aa=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}),Pa=Aa("computeActivityPhase"),Ca=Aa("computeDisplayPhase");var Qm=ke&&ke.__esModule?ke.default:ke;function io(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 Vi=new Set(["scale","translateX","translateY"]);function ji(e){return Object.fromEntries(Object.keys(Br.properties).filter(t=>!Vi.has(t)).map(t=>[t,e[t]]))}var so=10;function Wi(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/so:void 0}var Oi=oe(()=>import("./chunks/GraphTrackSettingsDialog-R3XOY32L.js"));function Ba(e){return M.compose("LinearGraphDisplay",In,La(),ct,M.model({type:M.literal("LinearGraphDisplay"),configuration:Vo(e),layoutEngine:ar(er,"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"),encoding:Q(t,"encoding"),size:Q(t,"size"),layers:Q(t,"layers"),facet:{field:Q(t,["facet","field"]),sort:Q(t,["facet","sort"]),columns:Q(t,["facet","columns"])},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&&Fe(o))??(r&&Pt(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=so*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 Ga({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return Ca({renderError:t.renderError,regionTooLarge:t.regionTooLarge,error:t.error},()=>Pa({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},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Wo(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(so*(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=mn(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||io(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&ln(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&&Tt(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?Ge(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});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;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&ir(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,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(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;L(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"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-et)?.total??0)+et;(t.facetGrid?.total??0)+et>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Ge(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Ge(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||io(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end),{encoding:i,...s}=t.grammar;return{...ji(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...s,color:i?.color,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!sr(o))return[];let n=Fe(o),a=Pt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${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=>[Oi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-GF64RZ6B.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();dt(o,{label:"Graph genome view",icon:rt,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!Tt(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:Rn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:Tn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...va(t)]}}))}function po(e){e.addDisplayType(()=>{let t=Ta();return Object.assign(new Ma({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Ba(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-RRAXTQFC.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:xe(t,o,r)}:e}var _i=V("MinigraphBubbleAdapter",{bubblesLocation:B("/path/to/graph.bb.bed.gz"),index:W("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Di}),Ia=_i;function co(e){e.addAdapterType(()=>new ee({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:Ia,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-2YTXBZYS.js").then(t=>t.default)}))}function Fa(e){let{uri:t,baseUri:o,csi:r,format:n}=e;return typeof t!="string"?e:n===2?{...e,graphLocation:{uri:`${t}${wt}`,baseUri:o},graphIndex:xe(`${t}${wt}`,o,r)}:{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:xe(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:xe(`${t}.links.bed.gz`,o,r)}}function zi(e){let{coarse:t,baseUri:o,csi:r}=e;return Re(Fa(typeof t=="object"&&t!==null?{...e,coarse:Fa({baseUri:o,csi:r,...t})}:e))}var $i=V("RgfaTabixCoarseTier",{uri:{type:"maybeString"},format:{type:"maybeNumber"},aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:B("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:W("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.tier.links.bed.gz"),linksIndex:W("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:W("RgfaCoarseGraphIndex")}),Ji=V("RgfaTabixAdapter",{segmentsLocation:B("/path/to/graph.segs.bed.gz"),segmentsIndex:W("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.links.bed.gz"),linksIndex:W("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:W("RgfaGraphIndex"),walksLocation:B(""),walksIndex:W("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:$i},{explicitlyTyped:!0,preProcessSnapshot:zi}),Ea=Ji;function uo(e){e.addAdapterType(()=>new ee({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Ea,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-RCGS6YVM.js").then(t=>t.default)}))}function Na(e){return e.viewType==="LinearGenomeView"&&[e.trackType].flat().includes("VariantTrack")}var Yi=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function Ui(e,t){return e?`Pinned to ${tt(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function Xi(e,t){let o=x(e),r=t.flatMap(n=>n?[vn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function qi(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return jo(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 Ln(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=Co(t),r=un(o)?Ge(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=()=>{Xi(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:Ui(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&&tt(n)===tt(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Yi.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 mo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof je&&Na(t)&&t.extendStateModel(qi),t))}function Ha(e){e.getElementTypesInGroup("display").some(o=>o instanceof je&&Na(o))||console.warn("jbrowse-plugin-graphgenomeviewer: no linear VariantTrack display is registered, so WalkFormsAdapter tracks get no pin or floor menu")}var Ki=V("WalkFormsAdapter",{walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:W("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:An},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:Re}),Va=Ki;function lo(e){e.addAdapterType(()=>new ee({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:Va,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-3M5A4JL3.js").then(t=>t.default)}))}var Qi=V("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:W("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Se.stepBudget},walkByteBudget:{type:"integer",defaultValue:Se.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:B(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Re}),ja=Qi;function go(e){e.addAdapterType(()=>new ee({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ja,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-576RE5OE.js").then(t=>t.default)}))}var Zi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function es(e){return kt(e).toLowerCase().endsWith(".gbz.db")}function ts(e){let t=e.adapter;return t?.type!==void 0&&gn.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function os(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Do(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function rs(e,t,o){let r=n=>Zo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&es(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Qo(e))return r("RgfaTabixAdapter");if(kt(e).endsWith(Oo)&&(t!==void 0||$o(e)))return r("RgfaTabixWalks")}}function ho(e){e.addToExtensionPoint("Core-preProcessTrackConfig",ts),e.addToExtensionPoint("Core-preProcessTrackConfig",os),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>rs(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Zi.has(o)?"GraphTrack":t(o,r))}function bo(e){let t;if(I(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function ns(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Wa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Oa(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>I(o)&&Array.isArray(o.displays)?o.displays.filter(r=>I(r)&&r.type==="LinearGraphDisplay"):[])}function Da(e,t,o){let r=[],n=Te(e),a=new Set(n.map(i=>I(i)?i.id:void 0));for(let i of n){if(I(i)&&i.id===t)for(let s of Oa(i)){let p=bo(s.hoverHighlight);p&&Wa(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of I(i)?[...Oa(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((c,m)=>{let S=bo(c);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(I(i)&&i.type==="GraphGenomeView"&&ns(i,t,a)){let s=bo(i.hoverHighlight);s&&Wa(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var as=xn()(e=>({highlight:{height:"100%",position:"absolute",background:Ue(e.palette.primary.main,.08),borderLeft:`1px solid ${Ue(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Ue(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),is=Rt(function({model:t,region:o}){let{classes:r}=as(),n=t.getHighlightCoords(o);return n?N("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),ss=Rt(function({model:t}){let{views:o}=x(t);return N(Fo,{children:Da([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>N(is,{model:t,region:n},`graph-hover-${r}`))})}),_a=ss;var ps="LinearGenomeView-TracksContainerComponent";function yo(e){e.contributeToExtensionPoint(ps,({model:t})=>N(_a,{model:t},"graphgenomeview-hover-highlight"))}function ds(e){return e.views(t=>({get adapterConfig(){return hn(t,t.parentTrack.configuration)}}))}function fo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof je&&ro.includes(t.name)&&t.extendStateModel(ds),t))}var za="GraphGenomeView";var $a="8.7.0";var wo=class extends Pn{constructor(){super(...arguments);this.name=za;this.version=$a}install(o){oo(o),po(o),no(o),ao(o),yo(o),uo(o),co(o),Dt(o),go(o),lo(o),mo(o),zt(o),ho(o),fo(o),o.addRpcMethod(()=>new _e(o)),o.addRpcMethod(()=>new De(o)),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o))}configure(o){Ha(o);try{Bo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:rt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{wo as default};
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