jbrowse-plugin-graphgenomeviewer 8.3.1 → 8.3.3

package/dist/chunks/{GraphGenomeView-VW3PEHFP.js → GraphGenomeView-TC3UNRFN.js}

@@ -1,4 +1,4 @@
-import{b as C}from"./chunk-EKGY6PG2.js";import"./chunk-IUBWMYUA.js";import"./chunk-5ZGRAPN5.js";import"./chunk-GIIUVBOH.js";import{p as d}from"./chunk-WA7FCDLQ.js";import"./chunk-MHIKXNVU.js";import"./chunk-AUQISDXJ.js";import"./chunk-PMM6BEKY.js";import"./chunk-NSBH4FIW.js";import"./chunk-PEE2MP7K.js";import"./chunk-DSKPOCCE.js";import"./chunk-YBLNN5FU.js";import"./chunk-QATGAV57.js";import"./chunk-NAC3EXT4.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-B2MJV7HN.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import{i as L}from"./chunk-NIEZKWQV.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-5Z4VIKXZ.js";import{a as h,b as e,c as r,d as i}from"./chunk-JMBDTNUR.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
+import{b as C}from"./chunk-MBGXXS3Z.js";import"./chunk-37XRCKBJ.js";import"./chunk-QY2UJ4TX.js";import"./chunk-2EDOJEF3.js";import{p as d}from"./chunk-DXJSOZY2.js";import"./chunk-52L7CQAG.js";import"./chunk-NLMAQYCK.js";import"./chunk-YVRZM7FP.js";import"./chunk-BI2RYKPA.js";import"./chunk-JBQSIRNH.js";import"./chunk-B6YUND32.js";import"./chunk-YBLNN5FU.js";import"./chunk-QCEM5AXZ.js";import"./chunk-ELO4G2TG.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import{i as L}from"./chunk-NIEZKWQV.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-5Z4VIKXZ.js";import{a as h,b as e,c as r,d as i}from"./chunk-JMBDTNUR.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,E=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),F=i(function({model:a}){let{classes:t}=E(),[m,w]=L("");function u(){let o=m.trim();o&&a.openGfaLocation({uri:o,locationType:"UriLocation"})}function M(o){let c=o.target.files?.[0];o.target.value="",c&&a.loadGFAFile(c,c.name)}return r(l,{className:t.paper,children:[e("div",{className:t.header,children:e(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",e("input",{type:"file",accept:".gfa,.gfa1,.gfa2,.gz",hidden:!0,onChange:o=>{M(o)}})]}),e(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[e(G,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{w(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),e(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),e("div",{className:t.footer,children:e(n,{size:"small",onClick:()=>{a.loadGFA(T,"Example graph")},children:"Load 4-node example"})}),a.error?e(s,{error:a.error}):null]})}),x=F;var B=i(function({model:a}){return a.hasGraph?e(C,{model:a}):a.canRetryLoad?e(f,{model:a}):r(h,{children:[a.isLoading?e(f,{model:a}):null,e("div",{hidden:a.isLoading,children:e(x,{model:a})})]})}),q=B;export{q as default};
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package/dist/chunks/{GraphTrackSettingsDialog-TT5TXM5I.js → GraphTrackSettingsDialog-JZBOLXZW.js}

@@ -1,4 +1,4 @@
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+import{a as G,b as L}from"./chunk-37XRCKBJ.js";import{b as v,c as x,p as f}from"./chunk-DXJSOZY2.js";import"./chunk-YVRZM7FP.js";import"./chunk-BI2RYKPA.js";import"./chunk-ELO4G2TG.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-NIEZKWQV.js";import{F as m,H as h,n as H}from"./chunk-5Z4VIKXZ.js";import{b as p,c as l,d as u}from"./chunk-JMBDTNUR.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=u(function({model:t}){let{classes:n}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?l("div",{className:n.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),t.recut()}}),p(h,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),M=F;var I=f()({section:{marginBottom:24}});function A(o){return o.split(/[\s,]+/).filter(t=>t!=="")}var N=(o,t)=>o.join(`
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-//# sourceMappingURL=GraphTrackSettingsDialog-TT5TXM5I.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-JZBOLXZW.js.map

package/dist/chunks/{HighlightColorDialog-R3EIOO2M.js → HighlightColorDialog-4VGVC7SN.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=HighlightColorDialog-R3EIOO2M.js.map
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+//# sourceMappingURL=HighlightColorDialog-4VGVC7SN.js.map

package/dist/chunks/{LinearGraphDisplay-OBD4R5G3.js → LinearGraphDisplay-6IO5ADGB.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=LinearGraphDisplay-OBD4R5G3.js.map
+import{a,b as i}from"./chunk-MBGXXS3Z.js";import"./chunk-37XRCKBJ.js";import"./chunk-QY2UJ4TX.js";import"./chunk-2EDOJEF3.js";import"./chunk-DXJSOZY2.js";import"./chunk-52L7CQAG.js";import"./chunk-NLMAQYCK.js";import"./chunk-YVRZM7FP.js";import"./chunk-BI2RYKPA.js";import"./chunk-JBQSIRNH.js";import"./chunk-B6YUND32.js";import"./chunk-YBLNN5FU.js";import"./chunk-QCEM5AXZ.js";import"./chunk-ELO4G2TG.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.js";import{b as o,d as t}from"./chunk-JMBDTNUR.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
+//# sourceMappingURL=LinearGraphDisplay-6IO5ADGB.js.map

package/dist/chunks/{MinigraphBubbleAdapter-QXISPSHM.js → MinigraphBubbleAdapter-X4VJ3AEX.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-PEE2MP7K.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-HAVM67SF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-B2MJV7HN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-QXISPSHM.js.map
+import{a as f,d as c,f as d}from"./chunk-JBQSIRNH.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-UMCYJHEB.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
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package/dist/chunks/{RgfaTabixAdapter-SVZ5SSEY.js → RgfaTabixAdapter-535GN32R.js}

@@ -1,2 +1,2 @@
-import{a as F}from"./chunk-73B6AYVV.js";import"./chunk-WO3MEQ25.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-QATGAV57.js";import"./chunk-NAC3EXT4.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-HAVM67SF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-B2MJV7HN.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
-//# sourceMappingURL=RgfaTabixAdapter-SVZ5SSEY.js.map
+import{a as F}from"./chunk-UZYU3HDD.js";import"./chunk-A4YJFEBE.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-QCEM5AXZ.js";import"./chunk-ELO4G2TG.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-UMCYJHEB.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
+//# sourceMappingURL=RgfaTabixAdapter-535GN32R.js.map

package/dist/chunks/{WalkFormsAdapter-6LK2XCHQ.js → WalkFormsAdapter-DAGNKDXV.js}

@@ -1,2 +1,2 @@
-import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-TMFUYJFG.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-HAVM67SF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-B2MJV7HN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-6LK2XCHQ.js.map
+import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-4CP5H6LQ.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-UMCYJHEB.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CCPRHM4X.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-DAGNKDXV.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-LA22PX4I.js → WalkTabixSyntenyAdapter-M453NH3L.js}

@@ -1,2 +1,2 @@
-import{a as K}from"./chunk-73B6AYVV.js";import{b as $,d as U,e as X,f as O,g as z,h as G}from"./chunk-G3L2L62S.js";import"./chunk-WO3MEQ25.js";import{a as q}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-QATGAV57.js";import"./chunk-NAC3EXT4.js";import{E as D,F as H,i as j}from"./chunk-HAVM67SF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as S,c as I,d as W,g as F,h as w,i as x}from"./chunk-B2MJV7HN.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as R}from"./chunk-J5RMHLFJ.js";var se=50;function re(r){let i=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=se&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(i.push(["X",a]),e++):i.push([t,a])}return i}function E(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function A(r,i){let e=r.get(i);return e===void 0?0:e.end-e.start}function V(r){let i=new Map,e=s=>{let n=A(r,s),o=i.get(n);return o===void 0&&(o="N".repeat(n),i.set(n,o)),o},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=E(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function v(r,i,e){let t=r.at(-1);e>0&&(t?.[0]===i?t[1]+=e:r.push([i,e]))}function Z(r){let i=t=>A(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+i(s)}),a};return(t,a)=>{let s=E(a),n=E(t),[o,l]=M(n,s,i),[u,f]=M(n.map(g=>g^1).reverse(),s,i),c=f>l,p=c?u:o,N=Math.max(l,f);if(N<B)return[];let h=e(s),d=e(n),y=g=>c?n.length-1-p[g][0]:p[g][0],m=[];p.forEach(([,g],k)=>{if(k>0){let[ee,te]=[y(k-1),y(k)].sort((ae,ne)=>ae-ne);v(m,"I",d[te]-d[ee+1]),v(m,"D",h[g]-h[p[k-1][1]+1])}v(m,"=",i(s[g]))});let[b,P]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:d[b],queryEnd:d[P+1],targetStart:h[p[0][1]],targetEnd:h[p.at(-1)[1]+1],strand:c?"-":"+",edits:m,sharedBases:N}]}}function oe(r){let i=new Map,e=new Set;r.ids.forEach((t,a)=>{i.has(t)?e.add(t):i.set(t,r.rev[a])});for(let t of e)i.delete(t);return i}function J(r){let i=new Map,e=t=>{let a=i.get(t);return a===void 0&&(a=oe(t),i.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,o=0;for(let[l,u]of e(t)){let f=s.get(l);f===u?n+=A(r,l):f!==void 0&&(o+=A(r,l))}return{same:n,opposite:o}}}function Q(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let{same:n,opposite:o}=t(a,s);return n>=B&&o>=B?e(a,s):i(a,s)}}var ie=1e4;function Y(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let n=i(a,s),o=n[0]?.strand,{same:l,opposite:u}=t(a,s);return o===void 0||Math.min(l,u)<ie?n:[...n,...e(a,s).filter(f=>f.strand!==o)]}}function C({chain:r,target:i,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=re(r.edits);return G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends ${constructor(){super(...arguments);this.walks=new K(D(this,["walksLocation"],["walksIndex"]),this);this.refNames=new H(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks 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e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?kt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>kt(Fe(t,pe(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(pe(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>ot(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(rt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(rt(o))&&n.add(rt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Xn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?sr(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:_n(n,t),adapterType:ze(n).type,assemblies:Qt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Zt(U(e),t.assemblyName);return 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rowVisitsNeeded(){return e.chosenLayoutMode==="walkrows"&&(e.walkRibbons||e.layerSet.has("walkBlocks")||e.walkRowOrder==="shared")},assemblySpellings(t){let{assemblyManager:n}=U(e),o=n.has(t)?n.get(t):void 0,r=e.sourceAdapter?.assemblyNameToPanSN??{},a=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...a,...a.flatMap(s=>r[s]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t=e.containingView;if(!t)return;let n=Qo(t,e.geneTrack?.trackId);return n.length?new Wr({filters:n,jexl:Mn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?er(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,r=e.drawsLoadedReference||n!==void 0&&Gn(t,[n])!==void 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t=e.sourceAdapter?.samplesTsvLocation;return t&&In(t)?t:void 0},get walkRowGroupFields(){return Mo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Eo(t,n),r=(e.graph?.paths??[]).map(a=>de(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:To(r.map(o)),unvalued:r.some(a=>o(a)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&Ne(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return wn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Lo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowRibbons(){let t=this.walkRowBars;if(!e.walkRibbons||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return bn(n,ye(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return yn(n,ye(n))},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Be(e.graph,n,t):[]},get bubbleHalos(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:dn(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return Ze(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Ve(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return e.drawsNodes||!!e.layoutResult?.tubeMap},get 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o={frame:0,finish:()=>{e(1)}},r=0,a=performance.now(),s=()=>{if(!t()){e(1),n();return}let i=performance.now();r+=Math.min(i-a,is),a=i;let c=Math.min(1,r/ss);e(us(c)),c<1?o.frame=requestAnimationFrame(s):n()};return o.frame=requestAnimationFrame(s),o}function hg(e,t,n,o){for(let[r,a]of Object.entries(e)){let s=t[r],i=n[r];!s||!i||a.forEach((c,d)=>{c.x=o===1?i[d].x:s[d].x+(i[d].x-s[d].x)*o,c.y=o===1?i[d].y:s[d].y+(i[d].y-s[d].y)*o})}}var hs=8,fs=19,ta=fe+fs,gs=48;function ws(e,t,n){if(!(!e||!t))return st(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var Bg=Zr.views(e=>({get paneCeiling(){return Math.max(nt,e.paneHeight??ao)},get fitRoom(){return e.host?this.canvasHeight:this.paneCeiling},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=this.fitRoom,o=(e.walkRowGroups?.sections.length??0)*vo;return it(t.rows.length+1,n-this.fitPadTop-j-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?Po(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return ws(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=we(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,r)=>({...o,y:t.rowY(r)})):n},get visibleRowLabels(){return this.drawnRowLabels.flatMap(({label:t,y:n})=>{let o=e.toScreen({x:0,y:n}).y;return o>=0&&o<=this.canvasHeight?[{label:t,y:n,top:o}]:[]})},get fitPadLeft(){return this.drawnRowLabels.reduce((t,n)=>Math.max(t,Vn(n.label,0).x1+6),j)},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?ge(n,this.walkRowPitch):void 0;return t?Pe(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,r=o?t.reference:t.rows.find(a=>a.name===n);return r?{label:r.label,readout:bo(r,o?void 0:t.reference,t.unit,r.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,r=this.walkRowPitch,a=this.walkRowPlacement;if(!o||!r||!a)return;let s=a.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][s],c=a.rowY(s)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=r.barPx/2+2&&d>=0&&d<=i.bp?s:void 0},get fitPadTop(){let t=Yo(e.tubeMapGenes);return j+Math.max(0,t-1)*jo+e.referenceStripZonePx},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(io/o,(this.paneCeiling-this.fitPadTop-j)/t.h):0},get facetSpec(){let{field:t,sort:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,sort:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,sort:o}=e.facetSetting;return t?qe(t.map(r=>r.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?Ue({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-ta)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ct+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-gs?t+2*ct:hs},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(nt,o.total+ta);let r=Math.max(nt,e.legendSize.height+2*ct+e.referenceStripZonePx),a=this.fitPads,s=a.top+a.bottom;if(e.pixelRows)return Math.min(n,Math.max(r,t.h+s));let i=e.paneWidth-a.left-a.right;return t.w>0&&i>0?Math.min(n,Math.max(r,t.h*Math.max(i/t.w,this.minFitScale)+s)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:J,top:J,right:J,bottom:J}:{left:this.fitPadLeft,top:this.fitPadTop,right:j,bottom:j}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,r=this.fitPads;return t?Le(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:r.left,padTop:r.top,padRight:r.right,padBottom:r.bottom}):void 0}})).views(e=>({viewportToBuild(){return Kn(ho(e),lo)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,po]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=nr();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:so)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:s}=e;if(!o||!r||!a||!s)return;Te(e.viewportDirty,e.positionsVersion);let i=Gt(()=>e.viewportToBuild()),c=tt({...Oe(a,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:r,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,edgeWidth:e.linkWidth,highlight:t,axis:Gt(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===a&&ea(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return Wo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Vo(t,o.id,o.length)??"not on this walk":void 0},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${Y(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?cn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,edgeWidth:e.linkWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?[...e.backboneGenes??[],...e.ownGeneFeatures??[]]:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,rowAnnotation:e.walkRowAnnotation,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps}}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var Sn=H(D("path",{d:"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z"}),"LineStyle");var na=H(D("path",{d:"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z"}),"CompareArrows");var oa=H(D("path",{d:"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2"}),"HighlightAlt");var bs="Linear genome view",ys="Linear synteny view",ks="No synteny track in this session aligns these assemblies";function ra({label:e,icon:t,entries:n,entryLabel:o,onSelect:r,disabledHelpText:a,nameTheOnlyEntry:s=!0}){let[i]=n,c=a?[{label:e,icon:t,disabled:!0,disabledHelpText:a,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:s?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:r(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(d=>({label:o(d),onClick:r(d)}))}]}function Jg({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:r}){let a=n[0]?.coverage??e.length;return[...ra({label:bs,icon:Sn,entries:t,entryLabel:s=>`${s.sample} ${ae(s)}`,onSelect:s=>()=>{o({location:s,assembly:s.sample})}}),...e.length>=2?ra({label:`${ys} (${a} assemblies)`,icon:na,entries:n,entryLabel:s=>s.coverage<a?`${s.name} (${s.coverage} of ${a})`:s.name,nameTheOnlyEntry:!1,disabledHelpText:ks,onSelect:s=>()=>{r(s.trackId)}}):[]]}function 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