npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.1.2 → 7.1.3 - Mend

jbrowse-plugin-graphgenomeviewer 7.1.2 → 7.1.3

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

@@ -1,7 +1,7 @@
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n=Math.floor(o.start),a=Math.ceil(o.end);return{...mi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&L(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Do(o))return[];let n=Fe(o),a=Tt(r),i=t.haplotypeNames,p=t.subgraphHaplotypes,s=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:p?p.length===0:!n&&!a,onClick:()=>{s([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:p===void 0,onClick:()=>{s(void 0)}}]:[],{type:"radio",label:"Chosen in Graph 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fi=Y("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:W("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:Z("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:W("/path/to/graph.tier.links.bed.gz"),linksIndex:Z("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wi=Y("RgfaTabixAdapter",{segmentsLocation:W("/path/to/graph.segs.bed.gz"),segmentsIndex:Z("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:W("/path/to/graph.links.bed.gz"),linksIndex:Z("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:W(""),walksIndex:Z("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Pe.stepBudget},walkByteBudget:{type:"integer",defaultValue:Pe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fi},{explicitlyTyped:!0,preProcessSnapshot:yi}),da=wi;function eo(e){e.addAdapterType(()=>new ce({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:da,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-PSKYWD2X.js").then(t=>t.default)}))}var Mi=Y("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:W("/path/to/graph.walks.bed.gz"),walksIndex:Z("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Pe.stepBudget},walkByteBudget:{type:"integer",defaultValue:Pe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:W(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Ke}),ua=Mi;function to(e){e.addAdapterType(()=>new ce({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-U53JLYVU.js").then(t=>t.default)}))}var ki=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Si(e){return ko(e).toLowerCase().endsWith(".gbz.db")}function Ri(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 xi(e,t,o){let r=n=>Po({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Si(e))return r("GbzBaseSyntenyAdapter");if((!o||o==="RgfaTabixAdapter")&&vo(e))return r("RgfaTabixAdapter")}function oo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Ri),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>xi(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>ki.has(o)?"GraphTrack":t(o,r))}function ma(e){let t;if(Q(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Ti(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function la(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Gi(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>Q(o)&&Array.isArray(o.displays)?o.displays.filter(r=>Q(r)&&r.type==="LinearGraphDisplay"):[])}function ha(e,t,o){let r=[],n=rt(e),a=new Set(n.map(i=>Q(i)?i.id:void 0));for(let i of n){if(Q(i)&&i.id===t)for(let p of Gi(i)){let s=ma(p.hoverHighlight);s&&la(s,o)&&r.push({key:typeof p.id=="string"?p.id:"graph-track",region:s})}if(Q(i)&&i.type==="GraphGenomeView"&&Ti(i,t,a)){let p=ma(i.hoverHighlight);p&&la(p,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:p})}}return r}var Li=en()(e=>({highlight:{height:"100%",position:"absolute",background:qe(e.palette.primary.main,.08),borderLeft:`1px solid ${qe(e.palette.primary.main,.4)}`,borderRight:`1px solid ${qe(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),vi=St(function({model:t,region:o}){let{classes:r}=Li(),n=t.getHighlightCoords(o);return n?N("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Pi=St(function({model:t}){let{views:o}=L(t);return N(uo,{children:ha([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>N(vi,{model:t,region:n},`graph-hover-${r}`))})}),ga=Pi;var Ai="LinearGenomeView-TracksContainerComponent";function ro(e){e.contributeToExtensionPoint(Ai,({model:t})=>N(ga,{model:t},"graphgenomeview-hover-highlight"))}function Ci(e){return e.views(t=>({get adapterConfig(){return Jr(t,t.parentTrack.configuration)}}))}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof cn&&Xt.includes(t.name)&&t.extendStateModel(Ci),t))}var ba="GraphGenomeView";var ya="7.1.2";var ao=class extends nn{constructor(){super(...arguments);this.name=ba;this.version=ya}install(o){Yt(o),Zt(o),Ut(o),Kt(o),ro(o),eo(o),Qt(o),Vt(o),to(o),jt(o),oo(o),no(o),o.addRpcMethod(()=>new Je(o)),o.addRpcMethod(()=>new $e(o)),o.addRpcMethod(()=>new ze(o)),o.addRpcMethod(()=>new _e(o))}configure(o){try{so(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:dt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{ao as default};
+`).then(()=>{o.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(r=>{o.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>nr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{L(e).queueDialog(a=>[or,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{L(e).queueDialog(a=>[rr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...oe(Xo.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Lt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=z(e.chosenLayoutMode),r=Kn.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${zt(o)}${o.value==="force"?` (${r})`:""}`,icon:Mn,subMenu:[...Vo.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?Kn.map(([i,p])=>({...a,label:`${zt(n)} (${p})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:zt(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:kn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:oe(Lt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:Uo,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[];for(let o of Qr({contributors:e.launchableAssemblies,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:r=>{e.showInLinearView(r)},onShowSynteny:r=>{e.showSyntenyView(r)}}))gt(t,o);return t}}));var bt=qn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Fe(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Do(o),n=L(e);return r===void 0?void 0:_o(Oe(n,r),Oe(n,t.assemblyName))},cutChangedFrom(t){let o=jo(z(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{}}}}));function $t(){return T.compose("GraphGenomeView",fn,bt,T.model({type:T.literal("GraphGenomeView"),gfaLocation:T.maybe(T.frozen()),loadedRegion:T.maybe(T.frozen()),loadedTrackId:T.optional(T.string,""),layoutMode:xt(ot),color:T.maybe(T.frozen()),size:T.maybe(T.frozen()),layers:T.maybe(T.frozen()),facet:T.maybe(T.frozen()),rows:T.maybe(T.frozen()),hover:xt(Be)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?L(e).tracks.find(t=>t.trackId===e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;return{clearGraph(){t(),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let o=e.loadedRegion;if(e.gfaLocation)return e.displayName||e.setDisplayName(We(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,o);if(!e.loadedTrackId||!o)return;let r=e.sourceAdapter,n=o.end-o.start,a=e.offReference(o);if(!r)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(a)e.setError(new Error(a));else if(n>e.maxRegionBp)e.setError(new Error(`Region too large (${be(n)}) \u2014 zoom in to view graph (max ${be(e.maxRegionBp)})`));else return e.cutSubgraph(r,o,e.cutOptions)}}}).actions(e=>({retryLoad(){e.load()},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},afterAttach(){e.graph||e.load(),A(e,V(()=>e.walkStrip,()=>{e.loadedTrackId&&!z(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ii=yn()({});function Jt(e){e.addViewType(()=>new bn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:$t(),launchKeys:ii,ReactComponent:pe(()=>import("./chunks/GraphGenomeView-LX7GDEDM.js"))}))}var Yt=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function si(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Yt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Xt(e){e.addTrackType(()=>{let t=Y("GraphTrack",{},{baseConfiguration:mn(e),explicitIdentifier:"trackId"}),o=new un({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:ln(e,"GraphTrack",t)});for(let r of si(e))o.addDisplayType(r);return o})}function Ut(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var yt=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var Zn=yt&&yt.__esModule?yt.default:yt;var Se=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],pi=e=>Se!=null&&e in Object(Se)?Se[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Qn=pi("trackHeightConfigSchemaFields"),gu=Se&&Se.__esModule?Se.default:Se;function ea(){return Y("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:T.enumeration("LayoutMode",ot),defaultValue:"auto"},color:{type:"frozen",defaultValue:{}},size:{type:"frozen",defaultValue:{field:"depth",value:6}},layers:{type:"frozen",defaultValue:{}},facet:{type:"frozen",defaultValue:{}},rows:{type:"frozen",defaultValue:{}},hover:{type:"stringEnum",model:T.enumeration("HoverHighlight",Be),defaultValue:"nodes"},...Qn({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var Re=JBrowseExports["@jbrowse/core/svg/svgReady"],ci=e=>Re!=null&&e in Object(Re)?Re[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ta=ci("computeSvgReady");var Ru=Re&&Re.__esModule?Re.default:Re;var ft=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var oa=ft&&ft.__esModule?ft.default:ft;var xe=JBrowseExports["@jbrowse/display-kit/plotMenu"],di=e=>xe!=null&&e in Object(xe)?xe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),ra=di("editPlotMenuItems");var Gu=xe&&xe.__esModule?xe.default:xe;var Te=JBrowseExports["@jbrowse/render-core/displayPhase"],na=e=>Te!=null&&e in Object(Te)?Te[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),aa=na("computeActivityPhase");var ia=na("computeDisplayStatusPhase"),vu=Te&&Te.__esModule?Te.default:Te;function Kt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var ui=new Set(["scale","translateX","translateY"]);function mi(e){return Object.fromEntries(Object.keys(ur.properties).filter(t=>!ui.has(t)).map(t=>[t,e[t]]))}var qt=10;function li(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/qt:void 0}var hi=pe(()=>import("./chunks/GraphTrackSettingsDialog-47PQ6LM7.js"));function sa(e){return T.compose("LinearGraphDisplay",pn,oa(),bt,T.model({type:T.literal("LinearGraphDisplay"),configuration:go(e),layoutEngine:Ho(Ao,"stress"),cutRegion:T.maybe(T.frozen()),coarseCut:T.optional(T.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:ie(t,"layoutMode"),color:ie(t,"color"),size:ie(t,"size"),layers:ie(t,"layers"),facet:ie(t,"facet"),rows:ie(t,"rows"),hover:ie(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Fe(o))??(r&&Tt(r))},get coarseAboveBpPerPx(){return li(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=qt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${be(o.end-o.start)}, max ${be(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ta({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return ia({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>aa({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))bo(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(qt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=zr(o,t.capFor(r),z(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=z(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Kt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&$r(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{q(t)&&t.recuts===a&&rn(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?st(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||z(o).cutMargins!==z(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await L(t).rpcManager.call(le(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});q(t)&&t.sourceAdapter===o&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutResult,a=t.layoutBounds;if(!n||!a||n.referenceAxis||n.pixelRows||n.tubeMap||t.facetGrid)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let i=o.bpPerPx/r.bpPerPx,p=t.translateY+t.scaleY*(a.minY+a.h/2);t.scale*=i,t.translateX=i*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=p-i*(p-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;A(t,()=>{o?.abort()}),A(t,V(()=>{let n=t.sourceAdapter;return n&&Oo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,name:"GraphHaplotypeNames"})),A(t,V(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),A(t,V(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;A(t,V(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),A(t,V(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-pt)?.total??0)+pt;(t.facetGrid?.total??0)+pt>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),A(t,V(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?st(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?st(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Kt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...mi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&L(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Wo(o))return[];let n=Fe(o),a=Tt(r),i=t.haplotypeNames,p=t.subgraphHaplotypes,s=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:p?p.length===0:!n&&!a,onClick:()=>{s([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:p===void 0,onClick:()=>{s(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(p?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){L(t).queueDialog(o=>[hi,{model:t,open:!0,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-GGJXJHCS.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();gt(o,{label:"Graph genome view",icon:dt,disabled:!t.graphViewSpec,disabledHelpText:"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:tn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:on,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...ra(t)]}}))}function Zt(e){e.addDisplayType(()=>{let t=ea();return Object.assign(new Zn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:sa(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:pe(()=>import("./chunks/LinearGraphDisplay-QLPIRKPR.js"))}),{adapterCapabilities:["getSubgraph"]})})}function gi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:He(t,o,r)}:e}var bi=Y("MinigraphBubbleAdapter",{bubblesLocation:D("/path/to/graph.bb.bed.gz"),index:Z("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:gi}),pa=bi;function Qt(e){e.addAdapterType(()=>new ce({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:pa,adapterMetadata:{category:"Graph 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fi=Y("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:D("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:Z("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:D("/path/to/graph.tier.links.bed.gz"),linksIndex:Z("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),wi=Y("RgfaTabixAdapter",{segmentsLocation:D("/path/to/graph.segs.bed.gz"),segmentsIndex:Z("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:D("/path/to/graph.links.bed.gz"),linksIndex:Z("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:D(""),walksIndex:Z("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Pe.stepBudget},walkByteBudget:{type:"integer",defaultValue:Pe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:fi},{explicitlyTyped:!0,preProcessSnapshot:yi}),da=wi;function eo(e){e.addAdapterType(()=>new ce({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:da,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-PSKYWD2X.js").then(t=>t.default)}))}var Mi=Y("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:D("/path/to/graph.walks.bed.gz"),walksIndex:Z("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Pe.stepBudget},walkByteBudget:{type:"integer",defaultValue:Pe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:D(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Ke}),ua=Mi;function to(e){e.addAdapterType(()=>new ce({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-GH6NYQTF.js").then(t=>t.default)}))}var ki=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Si(e){return ko(e).toLowerCase().endsWith(".gbz.db")}function Ri(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 xi(e,t,o){let r=n=>Po({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Si(e))return r("GbzBaseSyntenyAdapter");if((!o||o==="RgfaTabixAdapter")&&vo(e))return r("RgfaTabixAdapter")}function oo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Ri),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>xi(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>ki.has(o)?"GraphTrack":t(o,r))}function ma(e){let t;if(Q(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Ti(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function la(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Gi(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>Q(o)&&Array.isArray(o.displays)?o.displays.filter(r=>Q(r)&&r.type==="LinearGraphDisplay"):[])}function ha(e,t,o){let r=[],n=rt(e),a=new Set(n.map(i=>Q(i)?i.id:void 0));for(let i of n){if(Q(i)&&i.id===t)for(let p of Gi(i)){let s=ma(p.hoverHighlight);s&&la(s,o)&&r.push({key:typeof p.id=="string"?p.id:"graph-track",region:s})}if(Q(i)&&i.type==="GraphGenomeView"&&Ti(i,t,a)){let p=ma(i.hoverHighlight);p&&la(p,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:p})}}return r}var Li=en()(e=>({highlight:{height:"100%",position:"absolute",background:qe(e.palette.primary.main,.08),borderLeft:`1px solid ${qe(e.palette.primary.main,.4)}`,borderRight:`1px solid ${qe(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),vi=St(function({model:t,region:o}){let{classes:r}=Li(),n=t.getHighlightCoords(o);return n?N("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Pi=St(function({model:t}){let{views:o}=L(t);return N(uo,{children:ha([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>N(vi,{model:t,region:n},`graph-hover-${r}`))})}),ga=Pi;var Ai="LinearGenomeView-TracksContainerComponent";function ro(e){e.contributeToExtensionPoint(Ai,({model:t})=>N(ga,{model:t},"graphgenomeview-hover-highlight"))}function Ci(e){return e.views(t=>({get adapterConfig(){return Jr(t,t.parentTrack.configuration)}}))}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof cn&&Yt.includes(t.name)&&t.extendStateModel(Ci),t))}var ba="GraphGenomeView";var ya="7.1.3";var ao=class extends nn{constructor(){super(...arguments);this.name=ba;this.version=ya}install(o){Jt(o),Zt(o),Xt(o),Ut(o),ro(o),eo(o),Qt(o),Nt(o),to(o),Ht(o),oo(o),no(o),o.addRpcMethod(()=>new Je(o)),o.addRpcMethod(()=>new $e(o)),o.addRpcMethod(()=>new ze(o)),o.addRpcMethod(()=>new _e(o))}configure(o){try{so(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:dt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{ao as default};
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