jbrowse-plugin-graphgenomeviewer 4.0.1 → 4.0.3

package/README.md

@@ -79,11 +79,12 @@ variant map draws them as glyphs.
 A graph track's display is `LinearGraphDisplay`. It cuts the view's window plus
 a window-width each side and re-cuts once the view leaves the cut, keeping its
 sample rows in the order they were drawn. On a layout whose x is reference bp,
-such as Anchored or Sample rows, the graph draws under the view's own
-coordinates and pans and zooms with it. The force-directed, ordered and walk-row
-layouts draw in their own coordinates inside the track, fitted to it, with their
-own zoom in the track menu, the way a variant matrix does. The track menu also
-picks the layout, the colour, a walk to lift out, and opens the settings.
+such as Anchored, Sample rows, Walk rows or the Variant map, the graph draws
+under the view's own coordinates and pans and zooms with it. The force-directed
+and ordered layouts draw in their own coordinates inside the track, fitted to
+it, with their own zoom in the track menu, the way a variant matrix does. The
+track menu also picks the layout, the colour, a walk to lift out, and opens the
+settings.
 
 ```json
 {

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

@@ -1,3 +1,3 @@
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s.types.compose("GraphGenomeView",br.BaseViewModel,(0,wr.RenderLifecycleMixin)(),s.types.model({type:s.types.literal("GraphGenomeView"),layoutQuality:s.types.optional(s.types.number,2),linearLayout:s.types.optional(s.types.boolean,!1),layoutMode:s.types.optional(s.types.enumeration(ge),"force"),colorScheme:s.types.optional(s.types.enumeration(ce),"auto"),bubbleSpread:s.types.optional(s.types.enumeration(yt),"auto"),nodeWidth:s.types.optional(s.types.enumeration(Ft),"depth"),showBubbles:s.types.optional(s.types.boolean,!0),showDeletionEdges:s.types.optional(s.types.boolean,!1),showGenes:s.types.optional(s.types.boolean,!0),geneTrackId:s.types.optional(s.types.string,""),repeatTrackId:s.types.optional(s.types.string,""),repeatKey:s.types.optional(s.types.string,""),walkRowSamples:s.types.maybe(s.types.frozen()),highlightedPath:s.types.optional(s.types.string,""),referencePath:s.types.optional(s.types.string,""),showPerf:s.types.optional(s.types.boolean,!1),contigThickness:s.types.optional(s.types.number,6),connectorThickness:s.types.optional(s.types.number,2),darkMode:s.types.optional(s.types.boolean,!1),scale:s.types.optional(s.types.number,1),translateX:s.types.optional(s.types.number,0),translateY:s.types.optional(s.types.number,0),drawPaths:s.types.optional(s.types.boolean,!1),paneHeight:s.types.maybe(s.types.number),maxGraphNodes:s.types.optional(s.types.number,Qo),maxRegionBp:s.types.optional(s.types.number,Zo),loadedTrackId:s.types.optional(s.types.string,""),loadedRegion:s.types.maybe(s.types.frozen()),subgraphHaplotypes:s.types.maybe(s.types.frozen()),subgraphContext:s.types.optional(s.types.number,1),gfaLocation:s.types.maybe(s.types.frozen()),colorDomain:s.types.maybe(s.types.frozen()),connectedViewId:s.types.maybe(s.types.string),coarseCut:s.types.optional(s.types.boolean,!1)})).volatile(()=>({graph:void 0,layoutResult:void 0,indexBubbles:void 0,geneFeatures:void 0,repeatArrays:void 0,popStack:[],error:void 0,isLoading:!1,loadCanceled:!1,statusMessage:"",hoveredNode:null,hoveredEdge:null,selectedNode:null,viewportDirty:0,positionsVersion:0,geometryVersion:0,builtViewport:void 0,draggingNode:null,isPanning:!1,viewportOwner:"fit",hostPaneHeight:void 0,cutNote:void 0,recuts:0,viewportDirtyTimer:void 0,positionsDirtyFrame:0,lastFetchMs:void 0,lastLayoutMs:void 0,lastGeometryMs:void 0,lastGeometryStrokeCount:void 0})).views(e=>({get nodeById(){if(e.graph){let t=new Map;for(let n of e.graph.nodes)t.set(n.id,n);return t}},get nodeLengths(){let t=new Map;for(let n of e.graph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get hasGraph(){return e.graph!==void 0},get showLoading(){return e.error===void 0&&(e.isLoading||(e.graph!==void 0||!!(e.loadedTrackId&&e.loadedRegion)||!!e.gfaLocation)&&e.lastGeometryStrokeCount===void 0)},get canRetryLoad(){return!!(e.loadedTrackId&&e.loadedRegion)||!!e.gfaLocation},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?vt(e.layoutMode,e.graph):!1},get canAnchorLayout(){return e.graph?.nodes.some(t=>t.stable?.rank===0)??!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get pathLegend(){let t=e.graph?.paths;return e.drawPaths&&t&&Fe(t.length)?Ve(t):[]},get walkChoices(){let t=e.graph?.paths;return t?.length?Ve(t):[]},get walkHighlight(){return e.graph&&e.highlightedPath?Kn(e.graph,e.highlightedPath):void 0},get effectiveDrawPaths(){return e.drawPaths&&Fe(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get preferredReferencePath(){return e.referencePath===""?e.loadedRegion?.assemblyName:e.referencePath},get rampDomain(){return e.colorDomain??e.loadedRegion},get effectiveColorScheme(){return e.colorScheme!=="auto"?e.colorScheme:e.graph?.anchoredBy?"reference-position":"uniform"},get nodePositions(){return e.layoutResult?.nodePositions},get rowLabels(){return e.layoutResult?.rowLabels??[]},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?Sn(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get sourceAdapter(){let t=(0,G.getSession)(e).tracks.find(n=>n.trackId===e.loadedTrackId);return t?(0,$.readConfObject)(t,"adapter"):void 0},get assemblyTrackChoices(){let t=e.loadedRegion;return t?(0,G.getSession)(e).tracks.filter(n=>(0,$.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,$.readConfObject)(n,"name"),adapterType:(0,$.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>je.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Ye.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return zn(e.repeatTrackChoices,e.repeatTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)}})).views(e=>({get nodeNeighbors(){return e.graph?pe(e.graph):void 0},get nodeInk(){let{contigThickness:t,nodeWidth:n,nodeById:r}=e,o=e.graph?Vt(e.graph):0;return{maxHalfWidthPx:Ht(t,n)/2,halfWidthPx:a=>{let i=r?.get(a);return i?Et(i,t,n,o)/2:t/2}}},get deletions(){return e.graph&&e.layoutMode!=="walkrows"?Mt(e.graph):[]},get walkRowBars(){if(e.layoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=t?Be(e.graph,t,t.unit):Be(e.graph,e.loadedRegion);if(!n)return;let r=e.walkRowSamples,o=r?n.rows.filter(a=>r.includes(a.sample)).sort((a,i)=>r.indexOf(a.sample)-r.indexOf(i.sample)||a.label.localeCompare(i.label)):n.rows;return{...n,rows:$t(o,t?.calls)}},get drawnRowLabels(){let t=this.walkRowBars;return t?[t.reference,...t.rows].map((n,r)=>({label:n.label,y:r*20})):e.rowLabels},get bubbleGlyphs(){return(e.layoutMode==="variants"?e.bubbles:[]).map(n=>({bubble:n,...U(n)}))},get genePins(){Me(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&e.layoutMode!=="variants"&&e.layoutMode!=="walkrows"&&e.graph&&e.geneFeatures&&t?Tn(e.graph,e.geneFeatures,t):[]},get bubbleHalos(){Me(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||e.layoutMode==="variants"||e.layoutMode==="walkrows"||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(r=>[r.name,r.label]));return xn(e.graph,e.bubbles,t,r=>n.get(r)??r)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.graph?Dt(e.graph,e.rampDomain):void 0},get assemblyNames(){let t=e.loadedRegion;return t?[t.assemblyName]:[]},get scaleX(){return Je(e.scale,e.pixelRows).scaleX},get scaleY(){return Je(e.scale,e.pixelRows).scaleY},get axisScale(){return Je(e.scale,e.pixelRows)},get layoutBounds(){let t;if(e.layoutResult){let n=1/0,r=1/0,o=-1/0,a=-1/0;for(let l of Object.values(e.layoutResult.nodePositions))for(let x of l)n=Math.min(n,x.x),r=Math.min(r,x.y),o=Math.max(o,x.x),a=Math.max(a,x.y);let i=e.layoutResult.referenceAxis&&e.popStack.length===0?e.loadedRegion:void 0;i&&i.end>i.start&&(n=i.start,o=i.end);let c=this.walkRowBars,g=c&&e.layoutResult.extent?Pt(c):e.layoutResult.extent;g&&(o=Math.max(o,g.maxX),a=Math.max(a,g.maxY)),t={minX:n,minY:r,w:o-n,h:a-r}}return t},get canvasHeight(){if(e.viewportOwner==="host"&&e.hostPaneHeight!==void 0)return e.hostPaneHeight;let t=this.layoutBounds,n=e.width-_*2,r=Math.max(Ke,e.paneHeight??Yo);if(!t)return r;if(e.pixelRows){let o=e.layoutMode==="variants"?Xo:Ke;return Math.min(r,Math.max(o,t.h+_*2))}return t.w>0&&n>0?Math.min(r,Math.max(Ke,t.h*n/t.w+_*2)):r}})).views(e=>({get geneTrack(){return Rn(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 hoverHighlight(){let t,n=e.loadedRegion,r=e.hoveredNode,o=e.nodeById,a=e.nodeNeighbors;if(n&&r!==null&&o&&a){let i=me({nodeId:r,nodeById:o,neighbors:a});i&&(t={refName:n.refName,assemblyName:n.assemblyName,...i})}return t}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?ht(t):[];return t?_t(t,{maxGap:n.length>0?ft(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,G.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)}})).views(e=>({get launchableAssemblies(){return Wt(nr(e.contributingAssemblies,e.loadedRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.loadedRegion;return t!==void 0&&ne({views:[...(0,G.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),r=n?le(n):void 0,o=r?jt(e.assemblyResolver,r):void 0,a=e.loadedRegion,i=e.nodeById,c=e.nodeNeighbors,g=a&&i&&c?me({nodeId:t,nodeById:i,neighbors:c}):void 0,l=a&&g?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...g}:void 0;return{own:r&&o?{location:Ue(r),assembly:o}:void 0,reference:a&&l?{location:Ue(l),assembly:a.assemblyName}:void 0,highlight:a&&l?{location:l,assembly:a.assemblyName}:void 0}}})).views(e=>({get coarseAboveBpPerPx(){let n=e.sourceAdapter?.coarse?.aboveBpPerPx;return typeof n=="number"?n:void 0}})).views(e=>({get cutTier(){return e.coarseCut&&e.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(e=>({get regionCapBp(){return e.cutTier==="coarse"?1/0:e.maxRegionBp}})).views(e=>({get host(){let t;try{t=(0,G.getContainingView)(e)}catch{return}return t!==e&&ye(t)?t:void 0}})).views(e=>({get hostPlacesX(){let{host:t,loadedRegion:n,layoutResult:r}=e;return t!==void 0&&t.initialized&&n!==void 0&&r?.referenceAxis===!0&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostFrame(){let{host:t,loadedRegion:n}=e;return e.hostPlacesX&&t&&n?Cn(t,n):void 0}})).actions(e=>({setError(t){e.error=t,e.isLoading=!1},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,n,r){e.lastGeometryMs=t,e.lastGeometryStrokeCount=n,e.builtViewport=r,e.geometryVersion++},setLayoutQuality(t){e.layoutQuality=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.layoutMode=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let r=At(n,t);ia(n,r),e.graph=r}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setHighlightedPath(t){e.highlightedPath=t},setPaneHeight(t){e.paneHeight=t,e.viewportOwner==="host"&&(e.hostPaneHeight=t)},adoptTrack(t){e.loadedTrackId!==t&&(e.loadedTrackId=t,e.loadedRegion=void 0,e.coarseCut=!1,e.graph=void 0,e.layoutResult=void 0)},setSubgraphContext(t){e.subgraphContext=t},setWalkRowSamples(t){e.walkRowSamples=t},setSubgraphHaplotypes(t){e.subgraphHaplotypes=t},setMaxRegionBp(t){e.maxRegionBp=t},pairWithLinearView(t){let n=e.connectedViewId;n!==void 0&&te([...(0,G.getSession)(e).views]).some(o=>o.id===n)||(e.connectedViewId=t)},setHoveredNode(t){e.hoveredNode=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.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,G.getSession)(e),i=e.loadedRegion,c=i?me({nodeId:t,nodeById:r,neighbors:o}):void 0;(0,G.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:le(n)?.sample,contributingHaplotype:le(n)?.haplotype,carriedBy:n.samples?.join(", "),...i&&c?{refName:i.refName,assemblyName:i.assemblyName,start:c.start,end:c.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=qe(e.scale*t),i=a/e.scale;e.scale=a,e.translateX=n-(n-e.translateX)*i,e.pixelRows||(e.translateY=r-(r-e.translateY)*i)},setViewportDirty(){e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){let t=e.layoutBounds,n=e.width-_*2,r=e.canvasHeight-_*2;if(e.viewportOwner==="host"){t&&r>0&&(e.translateY=hr(t,r,e.scaleY));return}if(t&&n>0&&r>0&&(t.w>0||!e.pixelRows&&t.h>0)){let o=t.w>0?n/t.w:1/0,a=t.h>0?r/t.h:1/0,i=qe(e.pixelRows?o:Math.min(o,a));e.scale=i,e.translateX=_-t.minX*i+(n-t.w*i)/2,e.translateY=hr(t,r,e.pixelRows?1:i)}},clearPerfMetrics(){e.lastFetchMs=void 0,e.lastLayoutMs=void 0,e.lastGeometryMs=void 0,e.lastGeometryStrokeCount=void 0,e.builtViewport=void 0}})).actions(e=>({hostTransform(t,n){let r=e.viewportOwner!=="host";r&&(e.hostPaneHeight=e.canvasHeight,e.viewportOwner="host"),e.scale=t,e.translateX=n,r&&e.zoomToFit()},releaseHost(){e.viewportOwner==="host"&&(e.hostPaneHeight=void 0,e.layoutResult?.referenceAxis?e.viewportOwner="user":(e.viewportOwner="fit",e.zoomToFit()))}})).actions(e=>{function t(){clearTimeout(e.viewportDirtyTimer),e.viewportDirtyTimer=setTimeout(()=>{(0,s.isAlive)(e)&&e.setViewportDirty()},qo)}function n(){cancelAnimationFrame(e.positionsDirtyFrame),e.positionsDirtyFrame=requestAnimationFrame(()=>{(0,s.isAlive)(e)&&e.setPositionsDirty()})}return{moveNode(r,o,a){let i=e.layoutResult?.nodePositions;if(i?.[r]){for(let c of i[r])c.x+=o,c.y+=a;n()}},scheduleViewportDirty:t}}).actions(e=>{let t;function n(d,m){let k=(0,G.getSession)(e),{rpcManager:L}=k,R="graph",S=d.nodes.some(N);return L.call(R,"GraphComputeLayout",{graph:{nodes:S?jn(d,m):m.nodes,edges:d.edges},options:{quality:e.layoutQuality,linearLayout:e.linearLayout,...m.opts,...S?{rotateComponents:!1}:{}},signal:t?.signal,statusCallback:A=>{e.setStatusMessage((0,G.statusMessageText)(A)??"")}})}function r(d){let m=d.nodes.some(N);return`${e.layoutQuality}|${e.linearLayout}|${e.bubbleSpread}|${m}|${d.referencePath??""}`}function*o(d){let m=performance.now(),k=Bt(e.layoutMode).run(d,e.loadedRegion,e.host?e.layoutResult?.sampleRows:void 0);if(k)return{result:k,duration:performance.now()-m};let L=aa(d),R=r(d),S=L.get(R);if(S)return{result:S,duration:performance.now()-m};let A=wt(e.bubbleSpread),I=Gt(d),{result:V,duration:z}=yield n(I.graph,Ce(I.graph,A)),O=Ce(d,A),P=new Map(O.nodes.map(Y=>[Y.id,ie(O.opts,Y.length)])),C=Nt(V.nodePositions,I.runs,Y=>P.get(Y)??0),E={...V,nodePositions:d.nodes.some(N)?$n(d,C):C};return sa(L,R,E),{result:E,duration:z}}let a=0;function*i(d){let m=++a,k=()=>e.graph===d&&m===a,L=t?.signal,R;try{R=yield*o(d)}catch(A){if(!k()||L?.aborted)return!1;throw A}let S=k();return S&&(e.layoutResult=R.result,e.setLayoutMs(R.duration)),S}function*c(d,m,k=!1){e.setStatusMessage("Parsing GFA");let L=ze(d),R=It(In(L,m),e.preferredReferencePath);if(R.nodes.length===0)throw new Error(`No graph segments in ${m}`);if(R.nodes.length>e.maxGraphNodes)throw new Error(`Graph too large to draw: ${R.nodes.length.toLocaleString()} nodes (limit ${e.maxGraphNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`);let S=k?e.selectedNode:null;e.graph=R,e.indexBubbles=void 0,e.geneFeatures=void 0,e.repeatArrays=void 0,e.popStack=[],e.clearInteractionState(),S!==null&&e.nodeById?.has(S)&&(e.selectedNode=S),e.setStatusMessage("Computing layout"),yield*i(R)}let g=0;function l(){let d=++g;return t?.abort(),t=new AbortController,e.loadCanceled=!1,{isLive:()=>d===g,signal:t.signal}}function x(){return e.loadedTrackId?(0,G.getSession)(e).tracks.find(d=>d.trackId===e.loadedTrackId):void 0}function*M(d,m,k){let L=Uo(d);if(!(d.type!=="RgfaTabixAdapter"||L===void 0||e.cutTier==="coarse"))try{let R=yield(0,G.getSession)(e).rpcManager.call("graph","CoreGetFeatures",{adapterConfig:{type:"MinigraphBubbleAdapter",uri:`${L}.bubbles.bed.gz`,baseUri:d.baseUri,assemblyNameToPanSN:d.assemblyNameToPanSN},regions:[m]});k()&&(e.indexBubbles=R.map(S=>({refName:m.refName,start:S.get("start"),end:S.get("end"),segmentCount:S.get("segmentCount"),pathCount:S.get("pathCount")??0,inversion:S.get("inversion"),shortestAlleleLength:S.get("shortestAlleleLength"),longestAlleleLength:S.get("longestAlleleLength"),segments:S.get("segments"),shortestAllele:void 0,longestAllele:void 0})))}catch(R){console.warn("[GraphGenomeView] no bubble index for this graph",R)}}function*p(d,m,k){let L=(0,G.getSession)(e),R=d?L.tracks.find(S=>S.trackId===d):void 0;if(R)try{return yield L.rpcManager.call("graph","CoreGetFeatures",{adapterConfig:(0,$.readConfObject)(R,"adapter"),regions:[m]})}catch(S){console.warn(`[GraphGenomeView] no ${k} for this graph`,S);return}}function*u(d,m){let k=yield*p(e.geneTrack?.trackId,d,"genes");k&&m()&&(e.geneFeatures=Gn(k))}function*b(d,m){let k=yield*p(e.repeatTrack?.trackId,d,"repeats");k&&m()&&(e.repeatArrays=Un(k))}function*f(d,m,k={}){let{isLive:L,signal:R}=l(),S=x(),A=m.end-m.start,I=(S&&pr(ur(S),m.assemblyName))??(A>e.regionCapBp?`Region too large (${Ge(A)}) \u2014 zoom in to view graph (max ${Ge(e.regionCapBp)})`:void 0);if(I!==void 0){e.graph=void 0,e.layoutResult=void 0,e.isLoading=!1,e.error=new Error(I);return}e.isLoading=!0,e.error=void 0,e.setStatusMessage("Fetching subgraph");try{let V=(0,G.getSession)(e),{rpcManager:z}=V,O="graph",P=performance.now(),C=yield z.call(O,"GetSubgraph",{adapterConfig:d,region:m,opts:k,signal:R});if(!L())return;if(e.setFetchMs(performance.now()-P),!C)throw new Error("Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph");let E=K(m);if(yield*c(C,E,!0),!L())return;e.setStatusMessage("Reading annotations"),yield Promise.all([(0,s.flow)(M)(d,m,L),(0,s.flow)(u)(m,L),(0,s.flow)(b)(m,L)])}catch(V){L()&&(console.error("[GraphGenomeView.loadFromTabixSubgraph]",V),e.error=V)}finally{L()&&(e.isLoading=!1)}}function*h(){let d=e.loadedRegion,m=x();if(d&&e.loadedTrackId&&!m)e.error=new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`);else if(m&&d){let k=e.cutTier==="coarse";yield*f((0,$.readConfObject)(m,"adapter"),d,{hops:k?0:e.subgraphContext,haplotypes:e.subgraphHaplotypes,tier:k?"coarse":void 0})}}function*w(d,m,k){let{isLive:L,signal:R}=l();e.loadedTrackId="",e.loadedRegion=k,e.coarseCut=!1,e.isLoading=!0,e.error=void 0;try{let S=typeof m=="string"?m:yield m(R);L()&&(yield*c(S,d))}catch(S){L()&&(console.error("[GraphGenomeView.loadWholeGFA]",S),e.error=S)}finally{L()&&(e.isLoading=!1)}return L()}return{clearGraph(){t?.abort(),t=void 0,g++,a++,e.graph=void 0,e.layoutResult=void 0,e.loadedTrackId="",e.loadedRegion=void 0,e.coarseCut=!1,e.cutNote=void 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Qe(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return n.addView("GraphGenomeView",r),t})}var Er=y(ae(),1),Hr=y(Mr(),1);var Tr=y(B(),1),Ar=y(Nr(),1),et=y(D(),1);function Ir(){return(0,Tr.ConfigurationSchema)("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:et.types.enumeration("LayoutMode",ge),defaultValue:"auto"},colorScheme:{type:"stringEnum",model:et.types.enumeration("ColorScheme",ce),defaultValue:"auto"},...(0,Ar.trackHeightConfigSchemaFields)({defaultHeight:300,height:"the most the track takes; a layout shorter than it takes only what it needs"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var vr=y(ae(),1),j=y(B(),1),Br=y(q(),1),Te=y(oe(),1),Fr=y(Cr(),1),H=y(D(),1);var tt=y($e(),1);var ca=(0,vr.lazy)(()=>import("./chunks/GraphSettingsDialog-KQK4YZN5.js"));function Vr(e){let t=re();return 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Ae=(e,t)=>(0,Ie.ConfigurationSchema)(e,{indexType:{model:Wr.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),pa=(0,Ie.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ae("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ae("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),ma=(0,Ie.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ae("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ae("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:pa},{explicitlyTyped:!0,preProcessSnapshot:it}),zr=ma;function st(e){e.addAdapterType(()=>new Yr.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:it,configSchema:zr,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-7ZGKJJYW.js").then(t=>t.default)}))}var Ur=y(oe(),1),Kr=y(ao(),1),ct=y(oo(),1),qr=y(co(),1);function dt(e){return typeof e=="object"&&e!==null}function ga(e){let t;if(dt(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 la(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function ha(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Xr(e,t,n){let r=[],o=new Set(te(e).map(a=>dt(a)?a.id:void 0));for(let a of e)if(dt(a)&&a.type==="GraphGenomeView"&&la(a,t,o)){let i=ga(a.hoverHighlight);i&&ha(i,n)&&r.push({key:typeof 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pt=class extends to.default{constructor(){super(...arguments);this.name=Qr;this.version=eo}install(n){Ze(n),nt(n),Qe(n),ut(n),st(n),at(n),Ee(n),He(n),n.addRpcMethod(()=>new Z(n)),n.addRpcMethod(()=>new J(n))}configure(n){try{(0,no.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Kt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{pt as default};
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s.types.compose("GraphGenomeView",wo.BaseViewModel,(0,So.RenderLifecycleMixin)(),s.types.model({type:s.types.literal("GraphGenomeView"),layoutQuality:s.types.optional(s.types.number,2),linearLayout:s.types.optional(s.types.boolean,!1),layoutMode:s.types.optional(s.types.enumeration(me),"force"),colorScheme:s.types.optional(s.types.enumeration(ce),"auto"),bubbleSpread:s.types.optional(s.types.enumeration(wt),"auto"),nodeWidth:s.types.optional(s.types.enumeration(Vt),"depth"),showBubbles:s.types.optional(s.types.boolean,!0),showDeletionEdges:s.types.optional(s.types.boolean,!1),showGenes:s.types.optional(s.types.boolean,!0),geneTrackId:s.types.optional(s.types.string,""),repeatTrackId:s.types.optional(s.types.string,""),repeatKey:s.types.optional(s.types.string,""),walkRowSamples:s.types.maybe(s.types.frozen()),highlightedPath:s.types.optional(s.types.string,""),referencePath:s.types.optional(s.types.string,""),showPerf:s.types.optional(s.types.boolean,!1),contigThickness:s.types.optional(s.types.number,6),connectorThickness:s.types.optional(s.types.number,2),darkMode:s.types.optional(s.types.boolean,!1),scale:s.types.optional(s.types.number,1),translateX:s.types.optional(s.types.number,0),translateY:s.types.optional(s.types.number,0),drawPaths:s.types.optional(s.types.boolean,!1),paneHeight:s.types.maybe(s.types.number),maxGraphNodes:s.types.optional(s.types.number,ea),maxRegionBp:s.types.optional(s.types.number,Qr),loadedTrackId:s.types.optional(s.types.string,""),loadedRegion:s.types.maybe(s.types.frozen()),subgraphHaplotypes:s.types.maybe(s.types.frozen()),subgraphContext:s.types.optional(s.types.number,1),gfaLocation:s.types.maybe(s.types.frozen()),colorDomain:s.types.maybe(s.types.frozen()),connectedViewId:s.types.maybe(s.types.string),coarseCut:s.types.optional(s.types.boolean,!1)})).volatile(()=>({graph:void 0,layoutResult:void 0,indexBubbles:void 0,geneFeatures:void 0,repeatArrays:void 0,popStack:[],error:void 0,isLoading:!1,loadCanceled:!1,statusMessage:"",hoveredNode:null,hoveredEdge:null,selectedNode:null,viewportDirty:0,positionsVersion:0,geometryVersion:0,builtViewport:void 0,draggingNode:null,isPanning:!1,viewportOwner:"fit",hostPaneHeight:void 0,cutNote:void 0,recuts:0,viewportDirtyTimer:void 0,positionsDirtyFrame:0,lastFetchMs:void 0,lastLayoutMs:void 0,lastGeometryMs:void 0,lastGeometryStrokeCount:void 0})).views(e=>({get nodeById(){if(e.graph){let t=new Map;for(let n of e.graph.nodes)t.set(n.id,n);return t}},get nodeLengths(){let t=new Map;for(let n of e.graph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get hasGraph(){return e.graph!==void 0},get showLoading(){return e.error===void 0&&(e.isLoading||(e.graph!==void 0||!!(e.loadedTrackId&&e.loadedRegion)||!!e.gfaLocation)&&e.lastGeometryStrokeCount===void 0)},get canRetryLoad(){return!!(e.loadedTrackId&&e.loadedRegion)||!!e.gfaLocation},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Bt(e.layoutMode,e.graph):!1},get canAnchorLayout(){return e.graph?.nodes.some(t=>t.stable?.rank===0)??!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get pathLegend(){let t=e.graph?.paths;return e.drawPaths&&t&&Fe(t.length)?Ve(t):[]},get walkChoices(){let t=e.graph?.paths;return t?.length?Ve(t):[]},get walkHighlight(){return e.graph&&e.highlightedPath?qn(e.graph,e.highlightedPath):void 0},get effectiveDrawPaths(){return e.drawPaths&&Fe(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get preferredReferencePath(){return e.referencePath===""?e.loadedRegion?.assemblyName:e.referencePath},get rampDomain(){return e.colorDomain??e.loadedRegion},get effectiveColorScheme(){return e.colorScheme!=="auto"?e.colorScheme:e.graph?.anchoredBy?"reference-position":"uniform"},get nodePositions(){return e.layoutResult?.nodePositions},get rowLabels(){return e.layoutResult?.rowLabels??[]},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get poppedFrom(){return e.popStack.at(-1)},get derivedBubbles(){return e.graph?Ln(e.graph):[]}})).views(e=>({get bubbles(){return e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles}})).views(e=>({get sourceAdapter(){let t=(0,G.getSession)(e).tracks.find(n=>n.trackId===e.loadedTrackId);return t?(0,$.readConfObject)(t,"adapter"):void 0},get assemblyTrackChoices(){let t=e.loadedRegion;return t?(0,G.getSession)(e).tracks.filter(n=>(0,$.readConfObject)(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:(0,$.readConfObject)(n,"name"),adapterType:(0,$.readConfObject)(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>je.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Ye.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Yn(e.repeatTrackChoices,e.repeatTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)}})).views(e=>({get nodeNeighbors(){return e.graph?pe(e.graph):void 0},get nodeInk(){let{contigThickness:t,nodeWidth:n,nodeById:o}=e,r=e.graph?Et(e.graph):0;return{maxHalfWidthPx:Dt(t,n)/2,halfWidthPx:i=>{let a=o?.get(i);return a?Ht(a,t,n,r)/2:t/2}}},get deletions(){return e.graph&&e.layoutMode!=="walkrows"?Gt(e.graph):[]},get walkRowBars(){if(e.layoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=t?Be(e.graph,t,t.unit):Be(e.graph,e.loadedRegion);if(!n)return;let o=e.walkRowSamples,r=o?n.rows.filter(i=>o.includes(i.sample)).sort((i,a)=>o.indexOf(i.sample)-o.indexOf(a.sample)||i.label.localeCompare(a.label)):n.rows;return{...n,rows:_t(r,t?.calls)}},get drawnRowLabels(){let t=this.walkRowBars;return t?[t.reference,...t.rows].map((n,o)=>({label:n.label,y:o*20})):e.rowLabels},get bubbleGlyphs(){return(e.layoutMode==="variants"?e.bubbles:[]).map(n=>({bubble:n,...U(n)}))},get genePins(){Me(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&e.layoutMode!=="variants"&&e.layoutMode!=="walkrows"&&e.graph&&e.geneFeatures&&t?An(e.graph,e.geneFeatures,t):[]},get bubbleHalos(){Me(e.positionsVersion);let t=e.layoutResult?.nodePositions;if(!e.showBubbles||e.layoutMode==="variants"||e.layoutMode==="walkrows"||!e.graph||!t)return[];let n=new Map(e.walkChoices.map(o=>[o.name,o.label]));return Sn(e.graph,e.bubbles,t,o=>n.get(o)??o)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.graph?Ot(e.graph,e.rampDomain):void 0},get assemblyNames(){let t=e.loadedRegion;return t?[t.assemblyName]:[]},get scaleX(){return Ze(e.scale,e.pixelRows).scaleX},get scaleY(){return Ze(e.scale,e.pixelRows).scaleY},get axisScale(){return Ze(e.scale,e.pixelRows)},get layoutBounds(){let t;if(e.layoutResult){let n=1/0,o=1/0,r=-1/0,i=-1/0;for(let l of Object.values(e.layoutResult.nodePositions))for(let x of l)n=Math.min(n,x.x),o=Math.min(o,x.y),r=Math.max(r,x.x),i=Math.max(i,x.y);let a=e.layoutResult.referenceAxis&&e.popStack.length===0?e.loadedRegion:void 0;a&&a.end>a.start&&(n=a.start,r=a.end);let d=this.walkRowBars,g=d&&e.layoutResult.extent?Ct(d):e.layoutResult.extent;g&&(r=Math.max(r,g.maxX),i=Math.max(i,g.maxY)),t={minX:n,minY:o,w:r-n,h:i-o}}return t},get canvasHeight(){if(e.viewportOwner==="host"&&e.hostPaneHeight!==void 0)return e.hostPaneHeight;let t=this.layoutBounds,n=e.width-_*2,o=Math.max(qe,e.paneHeight??Xr);if(!t)return o;if(e.pixelRows){let r=e.layoutMode==="variants"?Ur:qe;return Math.min(o,Math.max(r,t.h+_*2))}return t.w>0&&n>0?Math.min(o,Math.max(qe,t.h*n/t.w+_*2)):o}})).views(e=>({get geneTrack(){return Mn(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 hoverHighlight(){let t,n=e.loadedRegion,o=e.hoveredNode,r=e.nodeById,i=e.nodeNeighbors;if(n&&o!==null&&r&&i){let a=ge({nodeId:o,nodeById:r,neighbors:i});a&&(t={refName:n.refName,assemblyName:n.assemblyName,...a})}return t}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?bt(t):[];return t?jt(t,{maxGap:n.length>0?yt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=(0,G.getSession)(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([i,a])=>[a,i])),r=i=>i!==void 0&&t.has(i)?t.get(i)?.name??i:void 0;return i=>r(o.get(i))??r(i)}})).views(e=>({get launchableAssemblies(){return Wt(oo(e.contributingAssemblies,e.loadedRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.loadedRegion;return t!==void 0&&ne({views:[...(0,G.getSession)(e).views],connectedViewId:e.connectedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?le(n):void 0,r=o?zt(e.assemblyResolver,o):void 0,i=e.loadedRegion,a=e.nodeById,d=e.nodeNeighbors,g=i&&a&&d?ge({nodeId:t,nodeById:a,neighbors:d}):void 0,l=i&&g?{sample:i.assemblyName,haplotype:void 0,refName:i.refName,...g}:void 0;return{own:o&&r?{location:Ue(o),assembly:r}:void 0,reference:i&&l?{location:Ue(l),assembly:i.assemblyName}:void 0,highlight:i&&l?{location:l,assembly:i.assemblyName}:void 0}}})).views(e=>({get coarseAboveBpPerPx(){let n=e.sourceAdapter?.coarse?.aboveBpPerPx;return typeof n=="number"?n:void 0}})).views(e=>({get cutTier(){return e.coarseCut&&e.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(e=>({get regionCapBp(){return e.cutTier==="coarse"?1/0:e.maxRegionBp}})).views(e=>({get host(){let t;try{t=(0,G.getContainingView)(e)}catch{return}return t!==e&&ye(t)?t:void 0}})).views(e=>({get hostPlacesX(){let{host:t,loadedRegion:n,layoutResult:o}=e;return t!==void 0&&t.initialized&&n!==void 0&&o?.referenceAxis===!0&&e.popStack.length===0&&!t.dynamicBlocks.contentBlocks.some(r=>r.refName===n.refName&&r.reversed)}})).views(e=>({get hostFrame(){let{host:t,loadedRegion:n}=e;return e.hostPlacesX&&t&&n?vn(t,n):void 0}})).actions(e=>({setError(t){e.error=t,e.isLoading=!1},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,n,o){e.lastGeometryMs=t,e.lastGeometryStrokeCount=n,e.builtViewport=o,e.geometryVersion++},setLayoutQuality(t){e.layoutQuality=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.layoutMode=t},setReferencePath(t){e.referencePath=t;let n=e.graph;if(n?.anchoredBy==="paths"){let o=It(n,t);sa(n,o),e.graph=o}},setDrawPaths(t){e.drawPaths=t},setShowPerf(t){e.showPerf=t},setColorScheme(t){e.colorScheme=t},setBubbleSpread(t){e.bubbleSpread=t},setNodeWidth(t){e.nodeWidth=t},setShowBubbles(t){e.showBubbles=t},setShowDeletionEdges(t){e.showDeletionEdges=t},setShowGenes(t){e.showGenes=t},setGeneTrackId(t){e.geneTrackId=t},setRepeatTrackId(t){e.repeatTrackId=t},setRepeatKey(t){e.repeatKey=t},setHighlightedPath(t){e.highlightedPath=t},setPaneHeight(t){e.paneHeight=t,e.viewportOwner==="host"&&(e.hostPaneHeight=t)},adoptTrack(t){e.loadedTrackId!==t&&(e.loadedTrackId=t,e.loadedRegion=void 0,e.coarseCut=!1,e.graph=void 0,e.layoutResult=void 0)},setSubgraphContext(t){e.subgraphContext=t},setWalkRowSamples(t){e.walkRowSamples=t},setSubgraphHaplotypes(t){e.subgraphHaplotypes=t},setMaxRegionBp(t){e.maxRegionBp=t},pairWithLinearView(t){let n=e.connectedViewId;n!==void 0&&te([...(0,G.getSession)(e).views]).some(r=>r.id===n)||(e.connectedViewId=t)},setHoveredNode(t){e.hoveredNode=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.hoveredEdge=null,e.selectedNode=null,e.draggingNode=null,e.isPanning=!1},showNodeDetails(t){let n=e.nodeById?.get(t),o=e.nodeById,r=e.nodeNeighbors;if(n&&o&&r){let i=(0,G.getSession)(e),a=e.loadedRegion,d=a?ge({nodeId:t,nodeById:o,neighbors:r}):void 0;(0,G.isSessionModelWithWidgets)(i)&&i.showWidget(i.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:le(n)?.sample,contributingHaplotype:le(n)?.haplotype,carriedBy:n.samples?.join(", "),...a&&d?{refName:a.refName,assemblyName:a.assemblyName,start:d.start,end:d.end}:{}}}))}},setTransform(t,n,o){let{host:r}=e;e.viewportOwner==="host"&&r?r.horizontalScroll(e.translateX-n):(e.viewportOwner="user",e.scale=Je(t),e.translateX=n),e.translateY=o},zoom(t,n,o){let{host:r}=e;if(e.viewportOwner==="host"&&r){r.zoomTo(r.bpPerPx/t,n);return}e.viewportOwner="user";let i=Je(e.scale*t),a=i/e.scale;e.scale=i,e.translateX=n-(n-e.translateX)*a,e.pixelRows||(e.translateY=o-(o-e.translateY)*a)},setViewportDirty(){e.viewportDirty++},setPositionsDirty(){e.positionsVersion++},zoomToFit(){let t=e.layoutBounds,n=e.width-_*2,o=e.canvasHeight-_*2;if(e.viewportOwner==="host"){t&&o>0&&(e.translateY=yo(t,o,e.scaleY));return}if(t&&n>0&&o>0&&(t.w>0||!e.pixelRows&&t.h>0)){let r=t.w>0?n/t.w:1/0,i=t.h>0?o/t.h:1/0,a=Je(e.pixelRows?r:Math.min(r,i));e.scale=a,e.translateX=_-t.minX*a+(n-t.w*a)/2,e.translateY=yo(t,o,e.pixelRows?1:a)}},clearPerfMetrics(){e.lastFetchMs=void 0,e.lastLayoutMs=void 0,e.lastGeometryMs=void 0,e.lastGeometryStrokeCount=void 0,e.builtViewport=void 0}})).actions(e=>({hostTransform(t,n){let o=e.viewportOwner!=="host";o&&(e.hostPaneHeight=e.canvasHeight,e.viewportOwner="host"),e.scale=t,e.translateX=n,o&&e.zoomToFit()},releaseHost(){e.viewportOwner==="host"&&(e.hostPaneHeight=void 0,e.layoutResult?.referenceAxis?e.viewportOwner="user":(e.viewportOwner="fit",e.zoomToFit()))}})).actions(e=>{function t(){clearTimeout(e.viewportDirtyTimer),e.viewportDirtyTimer=setTimeout(()=>{(0,s.isAlive)(e)&&e.setViewportDirty()},Jr)}function n(){cancelAnimationFrame(e.positionsDirtyFrame),e.positionsDirtyFrame=requestAnimationFrame(()=>{(0,s.isAlive)(e)&&e.setPositionsDirty()})}return{moveNode(o,r,i){let a=e.layoutResult?.nodePositions;if(a?.[o]){for(let d of a[o])d.x+=r,d.y+=i;n()}},scheduleViewportDirty:t}}).actions(e=>{let t;function n(c,m){let k=(0,G.getSession)(e),{rpcManager:L}=k,R="graph",S=c.nodes.some(N);return L.call(R,"GraphComputeLayout",{graph:{nodes:S?zn(c,m):m.nodes,edges:c.edges},options:{quality:e.layoutQuality,linearLayout:e.linearLayout,...m.opts,...S?{rotateComponents:!1}:{}},signal:t?.signal,statusCallback:A=>{e.setStatusMessage((0,G.statusMessageText)(A)??"")}})}function o(c){let m=c.nodes.some(N);return`${e.layoutQuality}|${e.linearLayout}|${e.bubbleSpread}|${m}|${c.referencePath??""}`}function*r(c){let m=performance.now(),k=Ft(e.layoutMode).run(c,e.loadedRegion,e.host?e.layoutResult?.sampleRows:void 0);if(k)return{result:k,duration:performance.now()-m};let L=ia(c),R=o(c),S=L.get(R);if(S)return{result:S,duration:performance.now()-m};let A=kt(e.bubbleSpread),I=Nt(c),{result:V,duration:W}=yield n(I.graph,Ce(I.graph,A)),O=Ce(c,A),P=new Map(O.nodes.map(Y=>[Y.id,ie(O.opts,Y.length)])),C=Tt(V.nodePositions,I.runs,Y=>P.get(Y)??0),E={...V,nodePositions:c.nodes.some(N)?_n(c,C):C};return da(L,R,E),{result:E,duration:W}}let i=0;function*a(c){let m=++i,k=()=>e.graph===c&&m===i,L=t?.signal,R;try{R=yield*r(c)}catch(A){if(!k()||L?.aborted)return!1;throw A}let S=k();return S&&(e.layoutResult=R.result,e.setLayoutMs(R.duration)),S}function*d(c,m,k=!1){e.setStatusMessage("Parsing GFA");let L=We(c),R=Pt(Pn(L,m),e.preferredReferencePath);if(R.nodes.length===0)throw new Error(`No graph segments in ${m}`);if(R.nodes.length>e.maxGraphNodes)throw new Error(`Graph too large to draw: ${R.nodes.length.toLocaleString()} nodes (limit ${e.maxGraphNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`);let S=k?e.selectedNode:null;e.graph=R,e.indexBubbles=void 0,e.geneFeatures=void 0,e.repeatArrays=void 0,e.popStack=[],e.clearInteractionState(),S!==null&&e.nodeById?.has(S)&&(e.selectedNode=S),e.setStatusMessage("Computing layout"),yield*a(R)}let g=0;function l(){let c=++g;return t?.abort(),t=new AbortController,e.loadCanceled=!1,{isLive:()=>c===g,signal:t.signal}}function x(){return e.loadedTrackId?(0,G.getSession)(e).tracks.find(c=>c.trackId===e.loadedTrackId):void 0}function*M(c,m,k){let L=Kr(c);if(!(c.type!=="RgfaTabixAdapter"||L===void 0||e.cutTier==="coarse"))try{let R=yield(0,G.getSession)(e).rpcManager.call("graph","CoreGetFeatures",{adapterConfig:{type:"MinigraphBubbleAdapter",uri:`${L}.bubbles.bed.gz`,baseUri:c.baseUri,assemblyNameToPanSN:c.assemblyNameToPanSN},regions:[m]});k()&&(e.indexBubbles=R.map(S=>({refName:m.refName,start:S.get("start"),end:S.get("end"),segmentCount:S.get("segmentCount"),pathCount:S.get("pathCount")??0,inversion:S.get("inversion"),shortestAlleleLength:S.get("shortestAlleleLength"),longestAlleleLength:S.get("longestAlleleLength"),segments:S.get("segments"),shortestAllele:void 0,longestAllele:void 0})))}catch(R){console.warn("[GraphGenomeView] no bubble index for this graph",R)}}function*p(c,m,k){let L=(0,G.getSession)(e),R=c?L.tracks.find(S=>S.trackId===c):void 0;if(R)try{return yield L.rpcManager.call("graph","CoreGetFeatures",{adapterConfig:(0,$.readConfObject)(R,"adapter"),regions:[m]})}catch(S){console.warn(`[GraphGenomeView] no ${k} for this graph`,S);return}}function*u(c,m){let k=yield*p(e.geneTrack?.trackId,c,"genes");k&&m()&&(e.geneFeatures=Nn(k))}function*b(c,m){let k=yield*p(e.repeatTrack?.trackId,c,"repeats");k&&m()&&(e.repeatArrays=Kn(k))}function*f(c,m,k={}){let{isLive:L,signal:R}=l(),S=x(),A=m.end-m.start,I=(S&&lo(mo(S),m.assemblyName))??(A>e.regionCapBp?`Region too large (${Ge(A)}) \u2014 zoom in to view graph (max ${Ge(e.regionCapBp)})`:void 0);if(I!==void 0){e.graph=void 0,e.layoutResult=void 0,e.isLoading=!1,e.error=new Error(I);return}e.isLoading=!0,e.error=void 0,e.setStatusMessage("Fetching subgraph");try{let V=(0,G.getSession)(e),{rpcManager:W}=V,O="graph",P=performance.now(),C=yield W.call(O,"GetSubgraph",{adapterConfig:c,region:m,opts:k,signal:R});if(!L())return;if(e.setFetchMs(performance.now()-P),!C)throw new Error("Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph");let E=K(m);if(yield*d(C,E,!0),!L())return;e.setStatusMessage("Reading annotations"),yield 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gt=class extends rr.default{constructor(){super(...arguments);this.name=nr;this.version=or}install(n){Qe(n),ot(n),et(n),pt(n),dt(n),it(n),Ee(n),He(n),n.addRpcMethod(()=>new Z(n)),n.addRpcMethod(()=>new J(n))}configure(n){try{(0,ar.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:qt,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{gt as default};
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