jbrowse-plugin-graphgenomeviewer 3.0.4 → 3.1.0

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

@@ -1,3 +1,3 @@
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Ar=(e,t)=>(0,st.ConfigurationSchema)(e,{indexType:{model:Tr.types.enumeration("IndexType",["TBI","CSI"]),type:"stringEnum",defaultValue:"TBI"},location:{type:"fileLocation",defaultValue:{uri:t,locationType:"UriLocation"}}}),Qo=(0,st.ConfigurationSchema)("RgfaTabixAdapter",{segmentsLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.segs.bed.gz",locationType:"UriLocation"}},segmentsIndex:Ar("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/graph.links.bed.gz",locationType:"UriLocation"}},linksIndex:Ar("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:dt}),Nr=Qo;function ct(e){e.addAdapterType(()=>new Ir.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:dt,configSchema:Nr,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph 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i=a(),s=r.contextMenuInfo,d=(0,F.getContainingTrack)(r);if(s){let g=(0,F.getContainingView)(r),w=g.displayedRegions[s.displayedRegionIndex],R=_r(e,d);if(w){let m=U({label:R?"Graph genome view (this segment)":"Graph genome view (this feature)",region:Er({refName:w.refName,assemblyName:w.assemblyName,start:s.item.startBp,end:s.item.endBp}),tracks:R?Dr(d,g):Ge(e,(0,F.getSession)(r),w.assemblyName,g),session:(0,F.getSession)(r),connectedViewId:g.id});for(let u of m)(0,gt.pushLaunchViewMenuItem)(i,u)}}return i}}}})),t))}var Or=y(Ve(),1),Ie=y(J(),1);var ca="Graph genome view (this selection)";function ua(e){return e.name==="LinearGenomeView"}function bt(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(ua(t)&&t.extendStateModel(n=>n.extend(r=>{let o=r.menuItems,a=r.rubberBandMenuItems;function i(){let s=r.assemblyNames[0];return s?Ge(e,(0,Ie.getSession)(r),s,r):[]}return{views:{menuItems(){let s=o();for(let d of 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pt(e){e.addAdapterType(()=>new $o.default({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",normalizeSnapshot:ut,configSchema:Oo,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-7ZGKJJYW.js").then(t=>t.default)}))}var Do=w(Z(),1),jo=w(ar(),1),lt=w(rr(),1),zo=w(sr(),1);function mt(e){return typeof e=="object"&&e!==null}function ua(e){let t;if(mt(e)){let{refName:n,start:o,end:r,assemblyName:a}=e;typeof n=="string"&&typeof o=="number"&&typeof r=="number"&&(t={refName:n,start:o,end:r,assemblyName:typeof a=="string"?a:void 0})}return t}function pa(e,t,n){let o=e.connectedViewId;return o===void 0||o===t||!n.has(o)}function ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function _o(e,t,n){let o=[],r=new Set(ie(e).map(a=>mt(a)?a.id:void 0));for(let a of e)if(mt(a)&&a.type==="GraphGenomeView"&&pa(a,t,r)){let i=ua(a.hoverHighlight);i&&ma(i,n)&&o.push({key:typeof a.id=="string"?a.id:"graph",region:i})}return o}var U=w(Q(),1),la=(0,zo.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:(0,jo.alpha)(e.palette.primary.main,.25),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),ga=(0,lt.observer)(function({model:t,region:n}){let{classes:o}=la(),r=t.getHighlightCoords(n);return r?(0,U.jsx)("div",{"data-testid":"graph-node-highlight",className:o.highlight,style:{left:r.left,width:r.width}}):null}),ha=(0,lt.observer)(function({model:t}){let{views:n}=(0,Do.getSession)(t);return(0,U.jsx)(U.Fragment,{children:_o([...n],t.id,t.assemblyNames).map(({key:o,region:r})=>(0,U.jsx)(ga,{model:t,region:r},`graph-hover-${o}`))})}),Wo=ha;var Yo=w(Q(),1),ba="LinearGenomeView-TracksContainerComponent";function gt(e){e.contributeToExtensionPoint(ba,({model:t})=>(0,Yo.jsx)(Wo,{model:t},"graphgenomeview-hover-highlight"))}var bt=w(B(),1),ht=w(Ve(),1),F=w(Z(),1);var Pe="Graph genome view (this region)";function Xo(e,t={start:0,end:1/0}){let n=Math.max(10,Math.floor((e.end-e.start)*.5));return{...e,start:Math.max(t.start,e.start-n),end:Math.min(t.end,e.end+n)}}function fa(e){return e.reduce((t,n)=>t&&t.end-t.start>=n.end-n.start?t:n,void 0)}function se(e){let t=fa(e);return t?{refName:t.refName,assemblyName:t.assemblyName,start:Math.max(0,Math.floor(t.start)),end:Math.floor(t.end)}:void 0}function Uo(e){let t=e.end-e.start;return t>X?`Region is ${O(t)} \u2014 zoom in or select a smaller range (max ${O(X)})`:void 0}function Ko({session:e,region:t,trackId:n,connectedViewId:o,haplotypes:r}){let a=t.end-t.start;a>X?e.notify(`Region too large (${O(a)}) \u2014 zoom in to open a graph view (max ${O(X)})`,"warning"):e.addView("GraphGenomeView",{displayName:`Graph \u2014 ${_(t)}`,loadedTrackId:n,loadedRegion:t,subgraphHaplotypes:r,connectedViewId:o,followLinearView:o!==void 0,...o===void 0?{}:{layoutMode:"auto"}})}function K({label:e,region:t,tracks:n,session:o,connectedViewId:r,navigate:a}){let i=[];if(t&&n.length>0){let s=Uo(t),p=m=>{let y=Ne(m.referenceAssembly,t.assemblyName)??s;return{disabled:y!==void 0,disabledHelpText:y,onClick:()=>{a?.(t),Ko({session:o,region:t,trackId:m.trackId,connectedViewId:r,haplotypes:m.haplotypes})}}};i=n.length===1?[{label:e,icon:te,...p(n[0])}]:[{label:e,icon:te,type:"subMenu",subMenu:n.map(m=>({label:m.name,...p(m)}))}]}return i}function ya(e){return e.name==="LinearBasicDisplay"}function qo(e,t){return Ze(e,(0,bt.getConf)(t,["adapter"]).type)}function Jo(e,t){return[et(e.configuration,(0,bt.getConf)(e,"trackId"),(0,F.getSession)(e),t)]}function ft(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(ya(t)&&t.extendStateModel(n=>n.extend(o=>{let r=o.trackMenuItems,a=o.contextMenuItems;return{views:{trackMenuItems(){let i=r(),s=(0,F.getContainingTrack)(o);if(qo(e,s)){let p=(0,F.getContainingView)(o);for(let m of K({label:Pe,region:se(p.dynamicBlocks.contentBlocks),tracks:Jo(s,p),session:(0,F.getSession)(o),connectedViewId:p.id}))(0,ht.pushLaunchViewMenuItem)(i,m)}return i},contextMenuItems(){let i=a(),s=o.contextMenuInfo,p=(0,F.getContainingTrack)(o);if(s){let m=(0,F.getContainingView)(o),y=m.displayedRegions[s.displayedRegionIndex],R=qo(e,p);if(y){let l=K({label:R?"Graph genome view (this segment)":"Graph genome view (this feature)",region:Xo({refName:y.refName,assemblyName:y.assemblyName,start:s.item.startBp,end:s.item.endBp},y),tracks:R?Jo(p,m):Te(e,(0,F.getSession)(o),y.assemblyName,m),session:(0,F.getSession)(o),connectedViewId:m.id,navigate:c=>{m.navTo(c)}});for(let c of l)(0,ht.pushLaunchViewMenuItem)(i,c)}}return i}}}})),t))}var Zo=w(Ve(),1),ve=w(Z(),1);var wa="Graph genome view (this selection)";function ka(e){return e.name==="LinearGenomeView"}function yt(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(ka(t)&&t.extendStateModel(n=>n.extend(o=>{let r=o.menuItems,a=o.rubberBandMenuItems;function i(){let s=o.assemblyNames[0];return s?Te(e,(0,ve.getSession)(o),s,o):[]}return{views:{menuItems(){let s=r();for(let p of K({label:Pe,region:se(o.dynamicBlocks.contentBlocks),tracks:i(),session:(0,ve.getSession)(o),connectedViewId:o.id}))(0,Zo.pushLaunchViewMenuItem)(s,p);return s},rubberBandMenuItems(){return[...a(),...K({label:wa,region:se(o.getSelectedRegions(o.leftOffset,o.rightOffset)),tracks:i(),session:(0,ve.getSession)(o),connectedViewId:o.id,navigate:s=>{o.navTo(s)}})]}}}})),t))}var Qo="GraphGenomeView";var er="3.1.0";var wt=class extends tr.default{constructor(){super(...arguments);this.name=Qo;this.version=er}install(n){at(n),it(n),ft(n),yt(n),gt(n),pt(n),ct(n),_e(n),De(n),n.addRpcMethod(()=>new oe(n)),n.addRpcMethod(()=>new ne(n))}configure(n){try{(0,nr.isAbstractMenuManager)(n.rootModel)&&n.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:te,onClick:o=>{o.addView("GraphGenomeView",{})}})}catch(o){console.warn("[GraphGenomeView] could not add the Add menu entry",o)}}};export{wt as default};
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