jbrowse-plugin-graphgenomeviewer 4.0.8 → 4.0.9

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

@@ -1,3 +1,3 @@
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va=(0,zr.defineLaunchKeys)()({});function st(e){e.addViewType(()=>new _r.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:it(),launchKeys:va,ReactComponent:(0,Or.lazy)(()=>import("./chunks/GraphGenomeView-K5PZO33Q.js"))}))}var jr=b(I(),1),$=b(z(),1);function Fa(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=n("MultiWaySyntenyDisplay");return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]})].filter(o=>o!==void 0)}function ut(e){e.addTrackType(()=>{let t=(0,jr.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,$.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new $.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,$.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Fa(e))n.addDisplayType(r);return n})}function ct(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return 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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 (${j(n.end-n.start)}, max ${j(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get 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va=(0,zr.defineLaunchKeys)()({});function st(e){e.addViewType(()=>new _r.default({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:it(),launchKeys:va,ReactComponent:(0,Or.lazy)(()=>import("./chunks/GraphGenomeView-K5PZO33Q.js"))}))}var jr=b(I(),1),$=b(z(),1);function Fa(e){let t=e.getElementTypesInGroup("display"),n=o=>t.find(a=>a.name===o),r=n("MultiWaySyntenyDisplay");return[n("LinearGraphDisplay"),n("LinearBasicDisplay"),r&&Object.assign(Object.create(r),{adapterCapabilities:["headerLanes"]})].filter(o=>o!==void 0)}function ut(e){e.addTrackType(()=>{let t=(0,jr.ConfigurationSchema)("GraphTrack",{},{baseConfiguration:(0,$.createBaseTrackConfig)(e),explicitIdentifier:"trackId"}),n=new $.TrackType({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:(0,$.createBaseTrackModel)(e,"GraphTrack",t)});for(let r of Fa(e))n.addDisplayType(r);return n})}function ct(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:n,...r}=t;return 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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 (${j(n.end-n.start)}, max ${j(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get displayPhase(){return(0,ve.computeDisplayStatusPhase)({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>(0,ve.computeActivityPhase)({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({setSubgraphContext(n){t.subgraphContext=n},setSubgraphHaplotypes(n){t.subgraphHaplotypes=n},setMaxRegionBp(n){t.maxRegionBp=n},cut(){let n=t.cutRegion;if(!n)return;let r=Ce(Ie(t.parentTrack.configuration),n.assemblyName);if(r){t.clearGraph(),t.setError(new Error(r));return}let o=t.cutTier==="coarse";return t.cutSubgraph(t.adapterConfig,n,{hops:o?0:t.subgraphContext,haplotypes:t.chosenHaplotypes,tier:o?"coarse":void 0})}})).actions(t=>({recutAt(n){let r=t.tierAt(n.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=qe(n,t.capFor(r),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(n){t.settledWindow=n;let r=O(t.chosenLayoutMode).cutMargins;return t.regionTooLarge||!t.loadCanceled&&t.tierAt(n.bpPerPx)===t.cutTier&&$n(t.cutRegion,n,r)?!1:(t.recutAt(n),!0)},switchLayout(n){let r=O(t.chosenLayoutMode).cutMargins;t.setLayoutMode(n);let o=t.host?Ke(t.host):void 0;return o&&!t.regionTooLarge&&O(n).cutMargins!==r?t.recutAt(o):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,R.addDisposer)(t,(0,Be.reaction)(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),(0,R.addDisposer)(t,(0,Be.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,R.addDisposer)(t,(0,Be.reaction)(()=>t.host?.coarseDynamicBlocks,n=>{let{host:r}=t,o=n&&r?Ke(r):void 0;o&&t.settleOn(o)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({trackMenuItems(){return[...t.graphMenuItems(),{label:"Settings",icon:an,onClick:()=>{(0,ro.getSession)(t).queueDialog(n=>[Ea,{model:t,open:!0,onClose:n}])}},...t.launchMenuItems()]}}))}function pt(e){e.addDisplayType(()=>{let t=qr();return Object.assign(new so.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ao(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,io.lazy)(()=>import("./chunks/LinearGraphDisplay-3WQBA6ZX.js"))}),{adapterCapabilities:["getSubgraph"]})})}var po=b(we(),1);var mt=b(I(),1),uo=b(V(),1);function gt(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 Va=(0,mt.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,mt.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:uo.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:gt}),co=Va;function lt(e){e.addAdapterType(()=>new po.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:gt,configSchema:co,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-FJIBTKQY.js").then(t=>t.default)}))}var bo=b(we(),1);var Ee=b(I(),1),lo=b(V(),1);function mo(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function go(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:mo(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:mo(`${t}.links.bed.gz`,n,r)}:e}function ht(e){let{coarse:t,baseUri:n}=e;return go(typeof t=="object"&&t!==null?{...e,coarse:go({baseUri:n,...t})}:e)}var Fe=(e,t)=>(0,Ee.ConfigurationSchema)(e,{indexType:{model:lo.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Ha=(0,Ee.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Fe("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Fe("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),Da=(0,Ee.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Fe("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Fe("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Ha},{explicitlyTyped:!0,preProcessSnapshot:ht}),ho=Da;function bt(e){e.addAdapterType(()=>new bo.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:ht,configSchema:ho,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-7ZGKJJYW.js").then(t=>t.default)}))}var Oa=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function _a(e){return"uri"in e?e.uri:"localPath"in e?e.localPath:e.name}function za(e){return _a(e).toLowerCase().endsWith(".gbz.db")}function ja(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 $a(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&za(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Gt(e))return Tt({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function yt(e){e.addToExtensionPoint("Core-preProcessTrackConfig",ja),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,o)=>$a(n,r,o)??t(n,r,o)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>Oa.has(n)?"GraphTrack":t(n,r))}var xo=b(U(),1),ko=b(Bo(),1),ft=b(Co(),1),So=b(Eo(),1);function W(e){return typeof e=="object"&&e!==null}function yo(e){let t;if(W(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 Wa(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function fo(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Xa(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>W(n)&&Array.isArray(n.displays)?n.displays.filter(r=>W(r)&&r.type==="LinearGraphDisplay"):[])}function wo(e,t,n){let r=[],o=new Set(re(e).map(a=>W(a)?a.id:void 0));for(let a of e){if(W(a)&&a.id===t)for(let i of Xa(a)){let s=yo(i.hoverHighlight);s&&fo(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph-track",region:s})}if(W(a)&&a.type==="GraphGenomeView"&&Wa(a,t,o)){let i=yo(a.hoverHighlight);i&&fo(i,n)&&r.push({key:typeof a.id=="string"?a.id:"graph",region:i})}}return r}var X=b(K(),1),Ya=(0,So.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,ko.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),Ua=(0,ft.observer)(function({model:t,region:n}){let{classes:r}=Ya(),o=t.getHighlightCoords(n);return o?(0,X.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:o.left,width:o.width}}):null}),Ka=(0,ft.observer)(function({model:t}){let{views:n}=(0,xo.getSession)(t);return(0,X.jsx)(X.Fragment,{children:wo([...n],t.id,t.assemblyNames).map(({key:r,region:o})=>(0,X.jsx)(Ua,{model:t,region:o},`graph-hover-${r}`))})}),Lo=Ka;var Mo=b(K(),1),qa="LinearGenomeView-TracksContainerComponent";function wt(e){e.contributeToExtensionPoint(qa,({model:t})=>(0,Mo.jsx)(Lo,{model:t},"graphgenomeview-hover-highlight"))}var Ro="GraphGenomeView";var Go="4.0.9";var xt=class extends To.default{constructor(){super(...arguments);this.name=Ro;this.version=Go}install(n){st(n),pt(n),ut(n),ct(n),wt(n),bt(n),lt(n),je(n),$e(n),yt(n),n.addRpcMethod(()=>new Q(n)),n.addRpcMethod(()=>new Z(n))}configure(n){try{(0,Ao.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:cn,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{xt as default};
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