jbrowse-plugin-graphgenomeviewer 5.0.0 → 5.0.1

package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

@@ -1,7 +1,7 @@
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e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?Wt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){ue(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||!this.drawsNodes||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return yi(e.graph,e.bubbles,t,r=>n.get(r)??r,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Me(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return Le(e.scale,e.pixelRows).scaleX},get scaleY(){return Le(e.scale,e.pixelRows).scaleY},get axisScale(){return Le(e.scale,e.pixelRows)},get layoutBounds(){let t=e.layoutResult,n=this.walkRowBars;return t?Ot(t,{region:e.popStack.length===0?e.graphRegion:void 0,extent:n&&t.extent?ht(n):void 0}):void 0}})).views(e=>({get geneTrack(){return Yt(e.geneTrackChoices,e.geneTrackId)},get deletionEdgeIndexes(){return new Map(e.deletions.map(t=>[t.edgeIndex,t.bypassed]))},get hiddenEdgeIndexes(){return new Set(e.showDeletionEdges?[]:e.deletions.map(t=>t.edgeIndex))},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,r=n?.tubeMap?n.nodePositions:void 0,o=!1,a=!1;if(t&&e.drawnGraph)for(let i of e.drawnGraph.nodes)r&&!r[i.id]||(t.midpoints.has(i.id)?i.stable&&i.stable.rank>0&&(o=!0):a=!0);return{offReference:o,unplaced:a}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?xi(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap?.pathColors,n=t&&this.tubeMapNodeColors?t.map((a,i)=>Fr(i,t.length)):t,r=new Set(e.hoveredRowWalks),o=e.drawnGraph?.paths;return n&&o&&r.size>0?n.map((a,i)=>r.has(o[i]?.name??"")?a:Hr):n},nodeSpan(t){let{nodeById:n,nodeNeighbors:r}=e;return n&&r?Se({nodeId:t,nodeById:n,neighbors:r}):void 0}})).views(e=>({get pathLegend(){let t=e.graph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&pn(t.length)?De(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?e.nodeSpan(t):n?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return t&&n?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var jn=w(J(),1);function te(e){return typeof e=="object"&&e!==null}function bc(e){return te(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function nt(e){return e.flatMap(t=>te(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function rt({views:e,connectedViewId:t,assemblyName:n}){let r=nt(e).filter(a=>bc(a)).filter(a=>a.assemblyNames.includes(n));return r.find(a=>a.id===t)??(r.length===1?r[0]:void 0)}function ot(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Ci(e,t,n){n.catch(r=>{console.error(`[GraphGenomeView] ${t}`,r),e.notifyError?.(`${t}: ${r}`,r)})}var yc=1e3;function Xn(e,t=yc){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function Ii(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function Ei({session:e,location:t,assembly:n,connectedViewId:r,tracks:o=[]}){let a=rt({views:e.views,connectedViewId:r,assemblyName:n}),i;return a?(Ci(e,`Could not show ${n} ${He(t)}`,Promise.resolve(a.navToLocString(Ct(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${He(t)}`,init:{assembly:n,loc:Ct(t),tracks:o}}).id,i}function Bi({session:e,location:t,assembly:n,connectedViewId:r}){let o=rt({views:e.views,connectedViewId:r,assemblyName:n});return o&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n}),o!==void 0}function Ni(e,t){if(t===void 0)return[];let n=e.tracks.find(o=>(0,jn.readConfObject)(o,"trackId")===t),r=n?(0,jn.readConfObject)(n,"assemblyNames"):[];return Array.isArray(r)?r.filter(o=>typeof o=="string").map(o=>ot(e,o)):[]}function Fi({session:e,contributors:t,trackId:n,graphTrackId:r}){let o=Ni(e,r),a=Ni(e,n),i=t.filter(c=>a.includes(c.sample)),s=i.length>=2?i:t,d={init:{views:s.map(c=>({assembly:c.sample,loc:Ct(c),...r!==void 0&&o.includes(c.sample)?{tracks:[r]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?Ci(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",d)):e.addView("LinearSyntenyView",d)}var Oi=Pi.views(e=>({get contributingAssemblies(){let t=e.graph,n=t?hr(t):[];return t?Eo(t,{maxGap:n.length>0?yr(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,we.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,r=new Map(Object.entries(n??{}).map(([a,i])=>[i,a])),o=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>o(r.get(a))??o(a)},get geneTracksByAssembly(){let t=new Map;for(let n of(0,we.getSession)(e).tracks){let r=(0,Kt.readConfObject)(n,"adapter").type;if(!et.has(r))continue;let o={trackId:n.trackId,name:(0,Kt.readConfObject)(n,"name"),adapterType:r};for(let a of(0,Kt.readConfObject)(n,"assemblyNames")){let i=ot((0,we.getSession)(e),a);t.set(i,[...t.get(i)??[],o])}}return new Map([...t].flatMap(([n,r])=>{let o=Yt(r,"");return o?[[n,o]]:[]}))}})).views(e=>({get launchableAssemblies(){return Bo(Ii(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&rt({views:[...(0,we.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),r=n?_e(n):void 0,o=r?We(e.assemblyResolver,r):void 0,a=e.graphRegion,i=e.nodeById,s=e.nodeNeighbors,d=a&&i&&s?Se({nodeId:t,nodeById:i,neighbors:s}):void 0,c=a&&d?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...d}:void 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t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Nt(e.nodePositions?.[t],n=>({x:n.x*e.scaleX+e.translateX,y:n.y*e.scaleY+e.translateY}))}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],r=0,o=0;for(let a of t.rows){if(!a.axis){o++;continue}let i=We(e.assemblyResolver,{sample:a.sample,haplotype:a.haplotype===void 0?void 0:`${a.sample}#${a.haplotype}`}),s=i?e.geneTracksByAssembly.get(i):void 0;if(!i||!s){r++;continue}n.push({row:a.name,trackId:s.trackId,region:{assemblyName:i,refName:a.axis.contig,...hn(a.axis,a.bp)}})}return{reads:n.slice(0,Cn),gaps:{untracked:r,unplaced:o,unread:Math.max(0,n.length-Cn)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowAt(t,n){let r=e.walkRowBars;if(!r)return;let o=Math.round((n-e.translateY)/(20*e.scaleY)),a=[r.reference,...r.rows][o],i=o*20*e.scaleY+e.translateY,s=(t-e.translateX)/e.scaleX-r.origin;return a&&Math.abs(n-i)<=ro/2+2&&s>=0&&s<=a.bp?o:void 0},walkRowLaunchTarget(t,n=e.walkRowBars){let r=n?[n.reference,...n.rows][t]:void 0;if(!r?.axis)return;let o=r.haplotype===void 0?void 0:`${r.sample}#${r.haplotype}`,a=t===0?e.graphRegion?.assemblyName:We(e.assemblyResolver,{sample:r.sample,haplotype:o});return{label:r.label,assembly:a,location:{sample:r.sample,haplotype:o,refName:r.axis.contig,...hn(r.axis,r.bp)}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?oo([t.reference,...t.rows],n):void 0}}));var Di=$i.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&H(e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(r=>r.refName===n.refName&&r.reversed)}})).views(e=>({get hostFrame(){let{host:t,graphRegion:n}=e;return e.hostPlacesX&&t&&n?Ve(t,n):void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?xo(t.layout):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t&&e.drawnGraph?fo(e.drawnGraph,t.layout):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap?.coarse,n=e.layoutResult?.tubeMap?.layout;return t&&n?Co(t.graph,n,t.deviations):[]},get tubeMapReferenceNodes(){let t=e.layoutResult;return t?.tubeMap&&!t.referenceAxis&&e.drawnGraph?yo(e.drawnGraph,t.tubeMap.layout):void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes?Mo(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;return 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te(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function rt(e){return e.flatMap(t=>te(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function ot({views:e,connectedViewId:t,assemblyName:n}){let r=rt(e).filter(a=>Mc(a)).filter(a=>a.assemblyNames.includes(n));return r.find(a=>a.id===t)??(r.length===1?r[0]:void 0)}function at(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Oi(e,t,n){n.catch(r=>{console.error(`[GraphGenomeView] ${t}`,r),e.notifyError?.(`${t}: ${r}`,r)})}var vc=1e3;function Yn(e,t=vc){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function Di(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function $i({session:e,location:t,assembly:n,connectedViewId:r,tracks:o=[]}){let a=ot({views:e.views,connectedViewId:r,assemblyName:n}),i;return a?(Oi(e,`Could not show ${n} ${He(t)}`,Promise.resolve(a.navToLocString(It(t),n))),i=a.id):i=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${He(t)}`,init:{assembly:n,loc:It(t),tracks:o}}).id,i}function Vi({session:e,location:t,assembly:n,connectedViewId:r}){let o=ot({views:e.views,connectedViewId:r,assemblyName:n});return o&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n}),o!==void 0}function Fi(e,t){if(t===void 0)return[];let n=e.tracks.find(o=>(0,zn.readConfObject)(o,"trackId")===t),r=n?(0,zn.readConfObject)(n,"assemblyNames"):[];return Array.isArray(r)?r.filter(o=>typeof o=="string").map(o=>at(e,o)):[]}function _i({session:e,contributors:t,trackId:n,graphTrackId:r}){let o=Fi(e,r),a=Fi(e,n),i=t.filter(c=>a.includes(c.sample)),s=i.length>=2?i:t,d={init:{views:s.map(c=>({assembly:c.sample,loc:It(c),...r!==void 0&&o.includes(c.sample)?{tracks:[r]}:{}})),tracks:n?s.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};e.launchView?Oi(e,"Could not open the 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t=(0,gs.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ce.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ce.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ce.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Cc(e))n.addDisplayType(r);return n})}function Zn(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Es=w($e(),1),Bs=w(fs(),1);var ws=w(J(),1),ks=w(ys(),1),Qn=w(re(),1);function xs(){return(0,ws.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:Qn.types.enumeration("LayoutMode",ft),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:Qn.types.enumeration("ColorScheme",bt),defaultValue:"auto"},...(0,ks.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var As=w($e(),1);var st=w(J(),1),Ps=w(le(),1),Ns=w(Gr(),1),tr=w(ie(),1),Cs=w(Rs(),1),B=w(re(),1),Ee=w(vs(),1);var it=w(ct(),1);var rn=w(ie(),1),Ie=w(re(),1);function Gs(e){return e instanceof Error&&(e.name==="NodeLimitError"||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Ls(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var er=class extends Error{constructor(){super("this window is too large to cut, and there is no overview to draw instead: either the haplotype index has none (rebuild it with gbz-haplotype-index 0.3 or later) or the reference has no path by this name. Zoom in to see the graph");this.name="NoOverviewError"}};function Ts(){return Ie.types.model({overviewRowsChoice:Ie.types.maybe(Ie.types.boolean)}).volatile(()=>({overview:void 0,overviewRegion:void 0,overviewBpPerPx:0,overviewLoading:!1,overviewError:void 0,overviewPainted:void 0,overviewController:void 0,dense:void 0})).views(e=>({get overviewAllRows(){return e.overviewRowsChoice??!0},get overviewCounts(){return e.overview&&e.overview.bin<=$o?Do(e.overview):void 0},overviewHolds(t){return e.overview!==void 0&&e.overviewError===void 0&&Pt(e.overviewRegion,t)&&t.bpPerPx>=e.overviewBpPerPx/2&&t.bpPerPx<=e.overviewBpPerPx*2}})).actions(e=>({setOverviewAllRows(t){e.overviewRowsChoice=t},beforeDestroy(){e.overviewController?.abort()},setOverviewPainted(t){e.overviewPainted=t},setDense(t){e.dense=t},forgetOverview(){e.overviewController?.abort(),e.overview=void 0,e.overviewRegion=void 0,e.overviewLoading=!1},fetchOverview:(0,Ie.flow)(function*(t,n,r){e.overviewController?.abort();let o=new AbortController;e.overviewController=o,e.overviewLoading=!0,e.overviewError=void 0;let a=At(n,1/0);try{let i=yield(0,rn.getSession)(e).rpcManager.call((0,rn.getRpcSessionId)(e),"GetHaplotypeOverview",{adapterConfig:t,region:a,bpPerPx:n.bpPerPx*2,haplotypes:r,signal:o.signal});o.signal.aborted||(e.overview=i,e.overviewRegion=a,e.overviewBpPerPx=n.bpPerPx,i||(e.overviewError=new er))}catch(i){o.signal.aborted||(console.error("[HaplotypeOverview]",i),e.overviewError=i instanceof Error?i:new Error(String(i)))}finally{e.overviewController===o&&(e.overviewLoading=!1)}})}))}var Ic=(0,As.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-2WPJRAJC.js"));function Is(e){return B.types.compose("LinearGraphDisplay",Ps.BaseDisplay,(0,Cs.default)(),en(),Ts(),B.types.model({type:B.types.literal("LinearGraphDisplay"),configuration:(0,st.ConfigurationReference)(e),pane:B.types.maybe(B.types.frozen()),cutRegion:B.types.maybe(B.types.frozen()),coarseCut:B.types.optional(B.types.boolean,!1),maxRegionBp:B.types.optional(B.types.number,Ze),subgraphContext:B.types.optional(B.types.number,1),subgraphHaplotypes:B.types.maybe(B.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get defaultLayoutMode(){return(0,st.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,st.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??is(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${he(n.end-n.start)}, max ${he(t.settledCapBp)})`:""},get overviewCapable(){return t.adapterConfig.type==="GbzBaseSyntenyAdapter"},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get showsOverview(){let n=t.settledWindow;return t.overviewCapable&&n!==void 0&&(t.regionTooLarge||Ls(t.dense,n))}})).views(t=>({get overviewPhase(){return(0,Ee.computeDisplayStatusPhase)({regionTooLarge:!1,error:t.overviewError},()=>(0,Ee.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.overviewLoading||!t.overview,fetchCanceled:!1,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.overview!==void 0&&t.overviewPainted===t.overview},()=>!0,()=>t.host?.effectiveBodyMounted??!0))},get displayPhase(){return t.showsOverview?this.overviewPhase:(0,Ee.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,Ee.computeActivityPhase)({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=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n,t.forgetOverview()},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.settledWindow;if(n&&t.showsOverview)return t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes);let r=t.cutRegion;if(!r)return;let o=nn(tn(t.parentTrack.configuration),r.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let a=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,r,{hops:a?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:a?"coarse":void 0,...H(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=At(n,t.capFor(r),H(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){if(t.settledWindow=n,t.showsOverview)return t.overviewHolds(n)||t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes),!1;let r=H(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Pt(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,B.isAlive)(t)&&t.overviewCapable&&Gs(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=H(t.chosenLayoutMode);t.setLayoutMode(n);let o=H(n),a=t.host?Tt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,B.addDisposer)(t,(0,it.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,B.addDisposer)(t,(0,it.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,B.addDisposer)(t,(0,it.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,B.addDisposer)(t,(0,it.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Tt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Tt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,B.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,tr.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Ns.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Et,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),...t.overviewCapable?[{label:"Zoomed out: every haplotype",subLabel:"Off draws only the lanes the track names",type:"checkbox",checked:t.overviewAllRows,onClick:()=>{t.setOverviewAllRows(!t.overviewAllRows)}}]:[],{label:"Settings",icon:Oo,onClick:()=>{(0,tr.getSession)(t).queueDialog(r=>[Ic,{model:t,open:!0,onClose:r}])}},...n]}}))}function nr(e){e.addDisplayType(()=>{let t=xs();return Object.assign(new Bs.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Is(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Es.lazy)(()=>import("./chunks/LinearGraphDisplay-7YE624D5.js"))}),{adapterCapabilities:["getSubgraph"]})})}var $s=w(Bt(),1);var rr=w(J(),1),Fs=w(re(),1);function or(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Ec=(0,rr.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,rr.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Fs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:or}),Os=Ec;function ar(e){e.addAdapterType(()=>new $s.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:or,configSchema:Os,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CZYQROL2.js").then(t=>t.default)}))}var Hs=w(Bt(),1);var an=w(J(),1),_s=w(re(),1);function Ds(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Vs(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Ds(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Ds(`${t}.links.bed.gz`,n,r)}:e}function ir(e){let{coarse:t,baseUri:n}=e;return Vs(typeof t=="object"&&t!==null?{...e,coarse:Vs({baseUri:n,...t})}:e)}var on=(e,t)=>(0,an.ConfigurationSchema)(e,{indexType:{model:_s.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Bc=(0,an.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:on("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:on("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Fc=(0,an.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:on("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:on("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Bc},{explicitlyTyped:!0,preProcessSnapshot:ir}),Ws=Fc;function sr(e){e.addAdapterType(()=>new Hs.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:ir,configSchema:Ws,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-BBWH5IPF.js").then(t=>t.default)}))}var Oc=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function $c(e){return Rr(e).toLowerCase().endsWith(".gbz.db")}function Dc(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Vc(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&$c(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Mr(e))return vr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function dr(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Dc),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>Vc(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Oc.has(n)?"GraphTrack":t(n,r))}var Ys=w(ie(),1),Us=w(sd(),1),cr=w(id(),1),Ks=w(cd(),1);function js(e){let t;if(te(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function _c(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Xs(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Wc(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>te(n)&&Array.isArray(n.displays)?n.displays.filter(r=>te(r)&&r.type==="LinearGraphDisplay"):[])}function zs(e,t,n){let r=[],o=nt(e),a=new Set(o.map(i=>te(i)?i.id:void 0));for(let i of o){if(te(i)&&i.id===t)for(let s of Wc(i)){let d=js(s.hoverHighlight);d&&Xs(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(te(i)&&i.type==="GraphGenomeView"&&_c(i,t,a)){let s=js(i.hoverHighlight);s&&Xs(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Be=w(Oe(),1),Hc=(0,Ks.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Us.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),jc=(0,cr.observer)(function({model:t,region:n}){let{classes:r}=Hc(),o=t.getHighlightCoords(n);return o?(0,Be.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Xc=(0,cr.observer)(function({model:t}){let{views:n}=(0,Ys.getSession)(t);return(0,Be.jsx)(Be.Fragment,{children:zs([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Be.jsx)(jc,{model:t,region:o},`graph-hover-${r}`))})}),qs=Xc;var Js=w(Oe(),1),zc="LinearGenomeView-TracksContainerComponent";function pr(e){e.contributeToExtensionPoint(zc,({model:t})=>(0,Js.jsx)(qs,{model:t},"graphgenomeview-hover-highlight"))}var Zs="GraphGenomeView";var Qs="5.0.0";var ur=class extends ed.default{constructor(){super(...arguments);this.name=Zs;this.version=Qs}install(n){qn(n),nr(n),Jn(n),Zn(n),pr(n),sr(n),ar(n),xn(n),Sn(n),dr(n),n.addRpcMethod(()=>new Ye(n)),n.addRpcMethod(()=>new ze(n)),n.addRpcMethod(()=>new je(n)),n.addRpcMethod(()=>new Xe(n))}configure(n){try{(0,td.isAbstractMenuManager)(n.rootModel)&&n.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{ur as default};
+`)&&(e.hoveredRowWalks=t)},setHoveredBubble(t){e.hoveredBubble=t},setPointerInPane(t){e.pointerInPane=t},setWalkStrip(t){e.walkStrip=t,e.stripHover=null},setStripHover(t){e.stripHover=t;let n=e.walkStripRows,r=e.walkStripFrame,o=t&&n?[n.reference,...n.rows].find(i=>i.name===t.row):void 0,a=o&&r&&e.graph?uo(e.graph,o,t.offset,r.scaleX):void 0;e.hoveredNode=a??null},setLegendSize(t){e.legendSize=t},setHoveredEdge(t){e.hoveredEdge=t},setSelectedNode(t){e.selectedNode=t},setDraggingNode(t){e.draggingNode=t},setPanning(t){e.isPanning=t},stopDragging(){e.draggingNode=null,e.isPanning=!1},clearInteractionState(){e.hoveredNode=null,e.hoveredBubble=null,e.hoveredEdge=null,e.selectedNode=null,e.draggingNode=null,e.isPanning=!1},showNodeDetails(t){let n=e.nodeById?.get(t),r=e.nodeById,o=e.nodeNeighbors;if(n&&r&&o){let a=(0,it.getSession)(e),i=e.graphRegion,s=i?Re({nodeId:t,nodeById:r,neighbors:o}):void 0;(0,it.isSessionModelWithWidgets)(a)&&a.showWidget(a.addWidget("BaseFeatureWidget","baseFeature",{featureData:{id:n.id,name:n.name,length:n.length,depth:n.depth,rank:n.stable?.rank,stableName:n.stable?.refName,contributingAssembly:_e(n)?.sample,contributingHaplotype:_e(n)?.haplotype,sampleCount:n.samples?.length,samples:n.samples,...i&&s?{refName:i.refName,assemblyName:i.assemblyName,start:s.start,end:s.end}:{}}}))}},setTransform(t,n,r){let{host:o}=e;e.viewportOwner==="host"&&o?o.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=qe(t),e.translateX=n),e.translateY=r},zoom(t,n,r){let{host:o}=e;if(e.viewportOwner==="host"&&o){o.zoomTo(o.bpPerPx/t,n);return}e.viewportOwner="user";let a=Na(e,t,n,r,e.pixelRows);e.scale=a.scale,e.translateX=a.translateX,e.translateY=a.translateY},setViewportDirty(){e.viewportRebuildPending=!1,e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){if(e.viewportOwner==="host"){let n=e.layoutBounds,r=e.facetGrid!==void 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Jn(){return U.types.compose("GraphGenomeView",ms.BaseViewModel,nn(),U.types.model({type:U.types.literal("GraphGenomeView"),gfaLocation:U.types.maybe(U.types.frozen()),loadedRegion:U.types.maybe(U.types.frozen()),loadedTrackId:U.types.optional(U.types.string,""),subgraphContext:U.types.optional(U.types.number,1),subgraphHaplotypes:U.types.maybe(U.types.frozen()),maxRegionBp:U.types.optional(U.types.number,Ze)})).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get cutHaplotypes(){return e.subgraphHaplotypes},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?(0,ls.getSession)(e).tracks.find(t=>t.trackId===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.launchMenuItems()}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let n=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(Fc(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,n);if(!e.loadedTrackId||!n)return;let r=e.sourceTrack,o=n.end-n.start,a=r?on(rn(r),n.assemblyName):void 0;if(!r)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(o>e.maxRegionBp)e.setError(new Error(`Region too large (${fe(o)}) \u2014 zoom in to view graph (max ${fe(e.maxRegionBp)})`));else return e.cutSubgraph(ge(e,r),n,{hops:e.subgraphContext,haplotypes:e.subgraphHaplotypes,...e.cutsWholeWalks?{snarls:"overlapping"}:{}})}}}).actions(e=>({retryLoad(){e.load()},switchLayout(t){let n=e.cutsWholeWalks;return e.setLayoutMode(t),e.loadedTrackId&&e.cutsWholeWalks!==n?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),(0,U.addDisposer)(e,(0,gs.reaction)(()=>e.walkStrip,()=>{e.loadedTrackId&&!H(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var Oc=(0,bs.defineLaunchKeys)()({});function Zn(e){e.addViewType(()=>new fs.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Jn(),launchKeys:Oc,ReactComponent:(0,hs.lazy)(()=>import("./chunks/GraphGenomeView-YYP4IFSI.js"))}))}var ys=y(J(),1),Ce=y(ue(),1),Qn=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Dc(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=o=>o&&Object.assign(Object.create(o),{adapterCapabilities:["headerLanes"]});return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),...Qn.map(o=>r(n(o)))].filter(o=>o!==void 0)}function er(e){e.addTrackType(()=>{let t=(0,ys.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,Ce.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new Ce.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,Ce.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Dc(e))n.addDisplayType(r);return n})}function tr(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Ds=y(De(),1),$s=y(ks(),1);var Rs=y(J(),1),Ms=y(Ss(),1),nr=y(re(),1);function vs(){return(0,Rs.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:nr.types.enumeration("LayoutMode",bt),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:nr.types.enumeration("ColorScheme",yt),defaultValue:"auto"},...(0,Ms.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Is=y(De(),1);var dt=y(J(),1),Es=y(ue(),1),Bs=y(Pr(),1),or=y(ae(),1),Fs=y(Ls(),1),B=y(re(),1),Ee=y(Ts(),1);var st=y(pt(),1);var an=y(ae(),1),Ie=y(re(),1);function Ps(e){return e instanceof Error&&(e.name==="NodeLimitError"||/reads more than nodeLimit|^Subgraph size limit of \d+ nodes exceeded/.test(e.message))}function Ns(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let n=e.end-e.start;return t.end-t.start>=n&&t.end>e.start-n&&t.start<e.end+n}var rr=class extends Error{constructor(){super("this window is too large to cut, and there is no overview to draw instead: either the haplotype index has none (rebuild it with gbz-haplotype-index 0.3 or later) or the reference has no path by this name. Zoom in to see the graph");this.name="NoOverviewError"}};function Cs(){return Ie.types.model({overviewRowsChoice:Ie.types.maybe(Ie.types.boolean)}).volatile(()=>({overview:void 0,overviewRegion:void 0,overviewBpPerPx:0,overviewLoading:!1,overviewError:void 0,overviewPainted:void 0,overviewController:void 0,dense:void 0})).views(e=>({get overviewAllRows(){return e.overviewRowsChoice??!0},get overviewCounts(){return e.overview&&e.overview.bin<=Wo?Ho(e.overview):void 0},overviewHolds(t){return e.overview!==void 0&&e.overviewError===void 0&&Nt(e.overviewRegion,t)&&t.bpPerPx>=e.overviewBpPerPx/2&&t.bpPerPx<=e.overviewBpPerPx*2}})).actions(e=>({setOverviewAllRows(t){e.overviewRowsChoice=t},beforeDestroy(){e.overviewController?.abort()},setOverviewPainted(t){e.overviewPainted=t},setDense(t){e.dense=t},forgetOverview(){e.overviewController?.abort(),e.overview=void 0,e.overviewRegion=void 0,e.overviewLoading=!1},fetchOverview:(0,Ie.flow)(function*(t,n,r){e.overviewController?.abort();let o=new AbortController;e.overviewController=o,e.overviewLoading=!0,e.overviewError=void 0;let a=Pt(n,1/0);try{let i=yield(0,an.getSession)(e).rpcManager.call((0,an.getRpcSessionId)(e),"GetHaplotypeOverview",{adapterConfig:t,region:a,bpPerPx:n.bpPerPx*2,haplotypes:r,signal:o.signal});o.signal.aborted||(e.overview=i,e.overviewRegion=a,e.overviewBpPerPx=n.bpPerPx,i||(e.overviewError=new rr))}catch(i){o.signal.aborted||(console.error("[HaplotypeOverview]",i),e.overviewError=i instanceof Error?i:new Error(String(i)))}finally{e.overviewController===o&&(e.overviewLoading=!1)}})}))}var $c=(0,Is.lazy)(()=>import("./chunks/GraphTrackSettingsDialog-2WPJRAJC.js"));function Os(e){return B.types.compose("LinearGraphDisplay",Es.BaseDisplay,(0,Fs.default)(),nn(),Cs(),B.types.model({type:B.types.literal("LinearGraphDisplay"),configuration:(0,dt.ConfigurationReference)(e),pane:B.types.maybe(B.types.frozen()),cutRegion:B.types.maybe(B.types.frozen()),coarseCut:B.types.optional(B.types.boolean,!1),maxRegionBp:B.types.optional(B.types.number,Ze),subgraphContext:B.types.optional(B.types.number,1),subgraphHaplotypes:B.types.maybe(B.types.frozen())})).preProcessSnapshot(t=>{let{pane:n,...r}=t;if(!n)return t;let{type:o,...a}=n;return{...a,...r}}).volatile(()=>({recuts:0,settledWindow:void 0})).views(t=>({get adapterConfig(){return ge(t,t.parentTrack.configuration)},get defaultLayoutMode(){return(0,dt.getConf)(t,"layoutMode")},get defaultColorScheme(){return(0,dt.getConf)(t,"colorScheme")},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get cutHaplotypes(){return this.chosenHaplotypes},get chosenHaplotypes(){return t.subgraphHaplotypes??us(t.parentTrack.configuration)},get coarseAboveBpPerPx(){let r=t.adapterConfig.coarse?.aboveBpPerPx;return typeof r=="number"?r:void 0}})).views(t=>({tierAt(n){let r=t.coarseAboveBpPerPx;return r!==void 0&&n>r?"coarse":"fine"},capFor(n){return n==="coarse"?1/0:t.maxRegionBp},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let n=t.settledWindow;return n?t.capFor(t.tierAt(n.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let n=t.settledWindow;return n!==void 0&&n.end-n.start>t.settledCapBp},get regionTooLargeReason(){let n=t.settledWindow;return n?`Region too large for a graph cut (${fe(n.end-n.start)}, max ${fe(t.settledCapBp)})`:""},get overviewCapable(){return t.adapterConfig.type==="GbzBaseSyntenyAdapter"},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get showsOverview(){let n=t.settledWindow;return t.overviewCapable&&n!==void 0&&(t.regionTooLarge||Ns(t.dense,n))}})).views(t=>({get overviewPhase(){return(0,Ee.computeDisplayStatusPhase)({regionTooLarge:!1,error:t.overviewError},()=>(0,Ee.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.overviewLoading||!t.overview,fetchCanceled:!1,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.overview!==void 0&&t.overviewPainted===t.overview},()=>!0,()=>t.host?.effectiveBodyMounted??!0))},get displayPhase(){return t.showsOverview?this.overviewPhase:(0,Ee.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,Ee.computeActivityPhase)({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=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n,t.forgetOverview()},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.settledWindow;if(n&&t.showsOverview)return t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes);let r=t.cutRegion;if(!r)return;let o=on(rn(t.parentTrack.configuration),r.assemblyName);if(o){t.clearGraph(),t.setError(new Error(o));return}let a=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,r,{hops:a?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:a?"coarse":void 0,...H(t.chosenLayoutMode).wholeWalks?{snarls:"overlapping"}:{}})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Pt(n,t.capFor(r),H(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){if(t.settledWindow=n,t.showsOverview)return t.overviewHolds(n)||t.fetchOverview(t.adapterConfig,n,t.chosenHaplotypes),!1;let r=H(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&Nt(t.cutRegion,n,r)?!1:(Promise.resolve(t.recutAt(n)).then(()=>{(0,B.isAlive)(t)&&t.overviewCapable&&Ps(t.error)&&this.refuseDenseCut(n)}),!0)},refuseDenseCut(n){t.setDense(n),t.cutRegion=void 0,this.settleOn(t.settledWindow??n)},switchLayout(n){let r=H(t.chosenLayoutMode);t.setLayoutMode(n);let o=H(n),a=t.host?Tt(t.host):void 0;return a&&!t.regionTooLarge&&(o.cutMargins!==r.cutMargins||o.wholeWalks!==r.wholeWalks)?t.recutAt(a):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({forceLoad(){let n=t.settledWindow;n&&(t.setMaxRegionBp(Math.ceil(n.end-n.start)),t.settleOn(n))},afterAttach(){t.cutRegion&&!t.graph&&t.cut(),(0,B.addDisposer)(t,(0,st.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,B.addDisposer)(t,(0,st.reaction)(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,r)=>n?.scale===r?.scale&&n?.translateX===r?.translateX,fireImmediately:!0,name:"GraphHostFrame"})),(0,B.addDisposer)(t,(0,st.reaction)(()=>`${t.facet.field} ${t.facetPlacement?.count}`,()=>{let n=t.facetGridIn(t.paneCeiling)?.total??0;(t.facetGrid?.total??0)>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),(0,B.addDisposer)(t,(0,st.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Tt(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let n=t.host?Tt(t.host):void 0,r=t.sourceTrackId;if(!n||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge)return;let o=Math.floor(n.start),a=Math.ceil(n.end);return{loadedTrackId:r,loadedRegion:{refName:n.refName,assemblyName:n.assemblyName,start:o,end:a},subgraphContext:t.subgraphContext,subgraphHaplotypes:t.chosenHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-o),layoutMode:t.chosenLayoutMode,colorScheme:t.chosenColorScheme,referencePath:t.referencePath,geneTrackId:t.geneTrackId,showGenes:t.showGenes,showBubbles:t.showBubbles,showDeletionEdges:t.showDeletionEdges,walkLayers:t.walkLayers,facet:(0,B.getSnapshot)(t.facet)}}})).actions(t=>({openGraphView(){let n=t.graphViewSpec;n&&(0,or.getSession)(t).addView("GraphGenomeView",n)}})).views(t=>({trackMenuItems(){let n=t.launchMenuItems();return(0,Bs.pushLaunchViewMenuItem)(n,{label:"Graph genome view",icon:Bt,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}}),[...t.graphMenuItems(),...t.overviewCapable?[{label:"Zoomed out: every haplotype",subLabel:"Off draws only the lanes the track names",type:"checkbox",checked:t.overviewAllRows,onClick:()=>{t.setOverviewAllRows(!t.overviewAllRows)}}]:[],{label:"Settings",icon:_o,onClick:()=>{(0,or.getSession)(t).queueDialog(r=>[$c,{model:t,open:!0,onClose:r}])}},...n]}}))}function ar(e){e.addDisplayType(()=>{let t=vs();return Object.assign(new $s.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Os(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Ds.lazy)(()=>import("./chunks/LinearGraphDisplay-7YE624D5.js"))}),{adapterCapabilities:["getSubgraph"]})})}var Ws=y(Ft(),1);var ir=y(J(),1),Vs=y(re(),1);function sr(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:r?"CSI":"TBI",location:{uri:`${t}.${r?"csi":"tbi"}`,baseUri:n}}}:e}var Vc=(0,ir.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,ir.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:Vs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:sr}),_s=Vc;function dr(e){e.addAdapterType(()=>new Ws.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:sr,configSchema:_s,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-CZYQROL2.js").then(t=>t.default)}))}var Ys=y(Ft(),1);var dn=y(J(),1),Xs=y(re(),1);function Hs(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function js(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Hs(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Hs(`${t}.links.bed.gz`,n,r)}:e}function cr(e){let{coarse:t,baseUri:n}=e;return js(typeof t=="object"&&t!==null?{...e,coarse:js({baseUri:n,...t})}:e)}var sn=(e,t)=>(0,dn.ConfigurationSchema)(e,{indexType:{model:Xs.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),_c=(0,dn.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Wc=(0,dn.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:sn("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:sn("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:_c},{explicitlyTyped:!0,preProcessSnapshot:cr}),zs=Wc;function pr(e){e.addAdapterType(()=>new Ys.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:cr,configSchema:zs,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-LQGQXCVO.js").then(t=>t.default)}))}var Hc=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function jc(e){return Lr(e).toLowerCase().endsWith(".gbz.db")}function Xc(e){let t=e.adapter;return t?.type==="GbzBaseSyntenyAdapter"&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function zc(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&jc(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Ar(e))return Tr({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function ur(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Xc),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>zc(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Hc.has(n)?"GraphTrack":t(n,r))}var Js=y(ae(),1),Zs=y(md(),1),mr=y(ud(),1),Qs=y(gd(),1);function Us(e){let t;if(te(e)){let{refName:n,start:r,end:o,assemblyName:a}=e;typeof n=="string"&&typeof r=="number"&&typeof o=="number"&&(t={refName:n,start:r,end:o,assemblyName:typeof a=="string"?a:void 0})}return t}function Yc(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function Ks(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Uc(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>te(n)&&Array.isArray(n.displays)?n.displays.filter(r=>te(r)&&r.type==="LinearGraphDisplay"):[])}function qs(e,t,n){let r=[],o=rt(e),a=new Set(o.map(i=>te(i)?i.id:void 0));for(let i of o){if(te(i)&&i.id===t)for(let s of Uc(i)){let d=Us(s.hoverHighlight);d&&Ks(d,n)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:d})}if(te(i)&&i.type==="GraphGenomeView"&&Yc(i,t,a)){let s=Us(i.hoverHighlight);s&&Ks(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Be=y(Oe(),1),Kc=(0,Qs.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Zs.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),qc=(0,mr.observer)(function({model:t,region:n}){let{classes:r}=Kc(),o=t.getHighlightCoords(n);return o?(0,Be.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Jc=(0,mr.observer)(function({model:t}){let{views:n}=(0,Js.getSession)(t);return(0,Be.jsx)(Be.Fragment,{children:qs([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,Be.jsx)(qc,{model:t,region:o},`graph-hover-${r}`))})}),ed=Jc;var td=y(Oe(),1),Zc="LinearGenomeView-TracksContainerComponent";function lr(e){e.contributeToExtensionPoint(Zc,({model:t})=>(0,td.jsx)(ed,{model:t},"graphgenomeview-hover-highlight"))}var nd=y(ue(),1);function Qc(e){return e.views(t=>({get adapterConfig(){return ge(t,t.parentTrack.configuration)}}))}function gr(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof nd.DisplayType&&Qn.includes(t.name)&&t.extendStateModel(Qc),t))}var rd="GraphGenomeView";var od="5.0.1";var hr=class extends ad.default{constructor(){super(...arguments);this.name=rd;this.version=od}install(n){Zn(n),ar(n),er(n),tr(n),lr(n),pr(n),dr(n),Rn(n),Mn(n),ur(n),gr(n),n.addRpcMethod(()=>new Ye(n)),n.addRpcMethod(()=>new ze(n)),n.addRpcMethod(()=>new je(n)),n.addRpcMethod(()=>new Xe(n))}configure(n){try{(0,id.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Bt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{hr as default};
 //# sourceMappingURL=jbrowse-plugin-graphgenomeviewer.esm.js.map