jbrowse-plugin-graphgenomeviewer 4.0.13 → 4.0.14

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

@@ -1,3 +1,3 @@
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aa(e){let{uri:t,baseUri:n,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:n},segmentsIndex:oa(`${t}.segs.bed.gz`,n,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:n},linksIndex:oa(`${t}.links.bed.gz`,n,r)}:e}function Dt(e){let{coarse:t,baseUri:n}=e;return aa(typeof t=="object"&&t!==null?{...e,coarse:aa({baseUri:n,...t})}:e)}var Ze=(e,t)=>(0,Je.ConfigurationSchema)(e,{indexType:{model:ia.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),ji=(0,Je.ConfigurationSchema)("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ze("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.tier.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ze("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),$i=(0,Je.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ze("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ze("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ji},{explicitlyTyped:!0,preProcessSnapshot:Dt}),sa=$i;function Ht(e){e.addAdapterType(()=>new da.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:Dt,configSchema:sa,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-NQEERXXI.js").then(t=>t.default)}))}var zi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Wi(e){return"uri"in e?Jt(e.uri).name:"localPath"in e?e.localPath:e.name}function Xi(e){return Wi(e).toLowerCase().endsWith(".gbz.db")}function Yi(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 Ui(e,t,n){if((!n||n==="GbzBaseSyntenyAdapter")&&Xi(e))return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:e,...t?{haplotypeIndexLocation:t}:{}};if((!n||n==="RgfaTabixAdapter")&&Qt(e))return en({choice:"RgfaTabixAdapter",loc:e,indexLoc:t,assembly:"",sample:""})}function Ot(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Yi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(n,r,a)=>Ui(n,r,a)??t(n,r,a)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(n,r)=>zi.has(n)?"GraphTrack":t(n,r))}var ma=S(ie(),1),ga=S(Ra(),1),_t=S(Ma(),1),la=S(Ga(),1);function re(e){return typeof e=="object"&&e!==null}function ca(e){let t;if(re(e)){let{refName:n,start:r,end:a,assemblyName:o}=e;typeof n=="string"&&typeof r=="number"&&typeof a=="number"&&(t={refName:n,start:r,end:a,assemblyName:typeof o=="string"?o:void 0})}return t}function qi(e,t,n){let r=e.connectedViewId;return r===void 0||r===t||!n.has(r)}function ua(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Ki(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(n=>re(n)&&Array.isArray(n.displays)?n.displays.filter(r=>re(r)&&r.type==="LinearGraphDisplay"):[])}function pa(e,t,n){let r=[],a=new Set(fe(e).map(o=>re(o)?o.id:void 0));for(let o of e){if(re(o)&&o.id===t)for(let i of Ki(o)){let s=ca(i.hoverHighlight);s&&ua(s,n)&&r.push({key:typeof i.id=="string"?i.id:"graph-track",region:s})}if(re(o)&&o.type==="GraphGenomeView"&&qi(o,t,a)){let i=ca(o.hoverHighlight);i&&ua(i,n)&&r.push({key:typeof o.id=="string"?o.id:"graph",region:i})}}return r}var oe=S(se(),1),Zi=(0,la.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,ga.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),Ji=(0,_t.observer)(function({model:t,region:n}){let{classes:r}=Zi(),a=t.getHighlightCoords(n);return a?(0,oe.jsx)("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:a.left,width:a.width}}):null}),Qi=(0,_t.observer)(function({model:t}){let{views:n}=(0,ma.getSession)(t);return(0,oe.jsx)(oe.Fragment,{children:pa([...n],t.id,t.assemblyNames).map(({key:r,region:a})=>(0,oe.jsx)(Ji,{model:t,region:a},`graph-hover-${r}`))})}),ha=Qi;var ba=S(se(),1),es="LinearGenomeView-TracksContainerComponent";function jt(e){e.contributeToExtensionPoint(es,({model:t})=>(0,ba.jsx)(ha,{model:t},"graphgenomeview-hover-highlight"))}var fa="GraphGenomeView";var ya="4.0.14";var $t=class extends wa.default{constructor(){super(...arguments);this.name=fa;this.version=ya}install(n){Nt(n),Ct(n),Pt(n),vt(n),jt(n),Ht(n),Vt(n),dt(n),ut(n),Ot(n),n.addRpcMethod(()=>new me(n)),n.addRpcMethod(()=>new pe(n)),n.addRpcMethod(()=>new ue(n))}configure(n){try{(0,xa.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Be,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{$t as default};
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