jbrowse-plugin-graphgenomeviewer 4.0.3 → 4.0.4

package/dist/chunks/{chunk-SDTCVLC3.js → chunk-RSAY56Y4.js}

@@ -1,4 +1,4 @@
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backbone",checked:o.showGenes,onClick:()=>{o.setShowGenes(!o.showGenes)}},{label:"Settings",icon:Kt,onClick:()=>{(0,Te.getSession)(n).queueDialog(a=>[ua,{model:o,open:!0,onClose:a}])}}]}})).actions(n=>({applyConfig(){let{pane:o,configured:r}=n;r.layoutMode||o.setLayoutMode((0,j.getConf)(n,"layoutMode")),r.colorScheme||o.setColorScheme((0,j.getConf)(n,"colorScheme")),r.height||o.setPaneHeight((0,j.getConf)(n,"height")),n.configured={layoutMode:!0,colorScheme:!0,height:!0}},resizeHeight(o){let r=n.height,i=Math.max(r+o,40);return n.pane.setPaneHeight(i),i-r}})).actions(n=>({afterAttach(){let{pane:o}=n;n.applyConfig(),o.adoptTrack(n.trackId),o.subgraphHaplotypes===void 0&&n.adapterConfig.type==="GbzBaseSyntenyAdapter"&&o.setSubgraphHaplotypes(go(n.parentTrack.configuration)),o.startHosting(),(0,H.addDisposer)(n,(0,at.autorun)(()=>{let{host:r}=n;r&&(o.setWidth(r.width),o.pairWithLinearView(r.id))},{name:"LinearGraphDisplayHost"})),(0,H.addDisposer)(n,(0,at.autorun)(()=>{let r=o.canvasHeight;n.height!==r&&n.setHeight(r)},{name:"LinearGraphDisplayHeight"}))}}))}function it(e){e.addDisplayType(()=>{let t=vo();return new $o.default({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Do(t),trackType:["FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:(0,Oo.lazy)(()=>import("./chunks/LinearGraphDisplay-7O3VQHKU.js"))})})}var zo=y(fe(),1);var st=y(B(),1),_o=y(D(),1);function dt(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:n},index:{indexType:o?"CSI":"TBI",location:{uri:`${t}.${o?"csi":"tbi"}`,baseUri:n}}}:e}var pa=(0,st.ConfigurationSchema)("MinigraphBubbleAdapter",{bubblesLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz",locationType:"UriLocation"}},index:(0,st.ConfigurationSchema)("MinigraphBubbleIndex",{indexType:{model:_o.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.bb.bed.gz.tbi",locationType:"UriLocation"}}}),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:dt}),jo=pa;function ct(e){e.addAdapterType(()=>new zo.default({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",normalizeSnapshot:dt,configSchema:jo,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-FJIBTKQY.js").then(t=>t.default)}))}var Ko=y(fe(),1);var Ie=y(B(),1),Xo=y(D(),1);function Wo(e,t,n){return{indexType:n?"CSI":"TBI",location:{uri:`${e}.${n?"csi":"tbi"}`,baseUri:t}}}function Yo(e){let{uri:t,baseUri:n,csi:o}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:Wo(`${t}.segs.bed.gz`,n,o),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:Wo(`${t}.links.bed.gz`,n,o)}:e}function ut(e){let{coarse:t,baseUri:n}=e;return Yo(typeof t=="object"&&t!==null?{...e,coarse:Yo({baseUri:n,...t})}:e)}var Ae=(e,t)=>(0,Ie.ConfigurationSchema)(e,{indexType:{model:Xo.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ga=(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:ga},{explicitlyTyped:!0,preProcessSnapshot:ut}),Uo=ma;function pt(e){e.addAdapterType(()=>new Ko.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:ut,configSchema:Uo,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-7ZGKJJYW.js").then(t=>t.default)}))}var Jo=y(re(),1),Zo=y(dr(),1),mt=y(sr(),1),Qo=y(pr(),1);function gt(e){return typeof e=="object"&&e!==null}function la(e){let t;if(gt(e)){let{refName:n,start:o,end:r,assemblyName:i}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof i=="string"?i:void 0})}return t}function ha(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function ba(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function qo(e,t,n){let o=[],r=new Set(te(e).map(i=>gt(i)?i.id:void 0));for(let i of e)if(gt(i)&&i.type==="GraphGenomeView"&&ha(i,t,r)){let a=la(i.hoverHighlight);a&&ba(a,n)&&o.push({key:typeof i.id=="string"?i.id:"graph",region:a})}return o}var z=y(X(),1),fa=(0,Qo.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,Zo.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),ya=(0,mt.observer)(function({model:t,region:n}){let{classes:o}=fa(),r=t.getHighlightCoords(n);return r?(0,z.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),wa=(0,mt.observer)(function({model:t}){let{views:n}=(0,Jo.getSession)(t);return(0,z.jsx)(z.Fragment,{children:qo([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,z.jsx)(ya,{model:t,region:r},`graph-hover-${o}`))})}),er=wa;var tr=y(X(),1),ka="LinearGenomeView-TracksContainerComponent";function lt(e){e.contributeToExtensionPoint(ka,({model:t})=>(0,tr.jsx)(er,{model:t},"graphgenomeview-hover-highlight"))}var nr="GraphGenomeView";var or="4.0.4";var ht=class extends rr.default{constructor(){super(...arguments);this.name=nr;this.version=or}install(n){nt(n),it(n),ot(n),lt(n),pt(n),ct(n),He(n),De(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:Zt,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{ht as default};
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