jbrowse-plugin-graphgenomeviewer 8.2.0 → 8.3.0

package/dist/chunks/{AddTrackWorkflow-7CXTSSMR.js → AddTrackWorkflow-JAIB6H2T.js}

@@ -1,2 +1,2 @@
-import{b as J,c as D,d as V,e as X,f as q,h as K}from"./chunk-5FNGR33G.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import{d as M,e as P}from"./chunk-3WG3GF2A.js";import{b as w,h as v,j as A,m as x}from"./chunk-J5RMHLFJ.js";import{i as o}from"./chunk-NIEZKWQV.js";import{A as O,B as j,C as z,F as h,a as H,f as E,g as c,o as B,s as N,t as W,u as _}from"./chunk-5Z4VIKXZ.js";import{b as a,c as f,d as I}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/core/util/tss-react"],oe=s=>n!=null&&s in Object(n)?n[s]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+s+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:s});var Q=oe("makeStyles"),ie=n&&n.__esModule?n.default:n;var se=Q()(s=>({paper:{margin:s.spacing(),padding:s.spacing()},field:{marginTop:s.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),re=["RgfaTabixAdapter","RgfaTabixWalks","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ne=I(function({model:t}){let{classes:i}=se(),y=A(t),d=M(t),[r,U]=o("RgfaTabixAdapter"),[l,Y]=o(),[k,G]=o(),[T,Z]=o(),m=r==="GbzBaseSyntenyAdapter",u=r==="RgfaTabixWalks",[C,$]=o(""),[R,ee]=o(""),[b,ae]=o("Pangenome graph"),[S,g]=o(),[F,L]=o(!1);async function te(){if(!l||!t.assembly)return;g(void 0),L(!0);let e=r==="RgfaTabixAdapter"?await J(l,v(t).pluginManager):void 0;if(L(!1),!(!P(t)||!t.assembly))try{let p=b.trim();w({model:t,session:y,conf:K({choice:r,loc:l,indexLoc:k,readsLoc:m?T:void 0,manifest:e,assembly:t.assembly,sample:C,haplotypes:u?q(R):void 0,trackId:x({name:p}),name:p})})}catch(p){g(p)}}return f(O,{className:i.paper,children:[S?a(E,{error:S}):null,f(N,{children:[a(_,{children:"File type"}),a(z,{value:r,onChange:e=>{U(e.target.value),G(void 0),g(void 0)},children:re.map(e=>a(W,{value:e,control:a(j,{}),label:D[e]},e))})]}),a(c,{location:l,name:V[r],rootModel:d,setLocation:Y}),a(c,{location:k,name:X[r],rootModel:d,setLocation:G}),m?a(c,{location:T,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:Z}):null,a(h,{className:i.field,value:C,onChange:e=>{$(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":u?"Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz":"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),u?a(h,{className:i.field,value:R,onChange:e=>{ee(e.target.value)},label:"Haplotypes",slotProps:{htmlInput:{"data-testid":"graph-haplotypes-input"}},helperText:"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file",placeholder:"HG002, HG00733",fullWidth:!0}):null,a(h,{className:i.field,value:b,label:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{ae(e.target.value)}}),a(H,{session:y,helperText:"Select assembly to add track to",selected:t.assembly,onChange:e=>{t.setAssembly(e)},fullWidth:!0}),a(B,{variant:"contained",className:i.submit,disabled:!l||!b.trim()||!t.assembly||F,onClick:()=>{te()},children:F?"Reading graph.json\u2026":"Submit"})]})}),ye=ne;export{ye as default};
-//# sourceMappingURL=AddTrackWorkflow-7CXTSSMR.js.map
+import{b as J,c as D,d as V,e as X,f as q,h as K}from"./chunk-ZEE3HTOT.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import{d as M,e as P}from"./chunk-3WG3GF2A.js";import{b as w,h as v,j as A,m as x}from"./chunk-J5RMHLFJ.js";import{i as o}from"./chunk-NIEZKWQV.js";import{A as O,B as j,C as z,F as h,a as H,f as E,g as c,o as B,s as N,t as W,u as _}from"./chunk-5Z4VIKXZ.js";import{b as a,c as f,d as I}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/core/util/tss-react"],oe=s=>n!=null&&s in Object(n)?n[s]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+s+"' from '@jbrowse/core/util/tss-react' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:s});var Q=oe("makeStyles"),ie=n&&n.__esModule?n.default:n;var se=Q()(s=>({paper:{margin:s.spacing(),padding:s.spacing()},field:{marginTop:s.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),re=["RgfaTabixAdapter","RgfaTabixWalks","GbzBaseSyntenyAdapter","MinigraphBubbleAdapter"],ne=I(function({model:t}){let{classes:i}=se(),y=A(t),d=M(t),[r,U]=o("RgfaTabixAdapter"),[l,Y]=o(),[k,G]=o(),[T,Z]=o(),m=r==="GbzBaseSyntenyAdapter",u=r==="RgfaTabixWalks",[C,$]=o(""),[R,ee]=o(""),[b,ae]=o("Pangenome graph"),[S,g]=o(),[F,L]=o(!1);async function te(){if(!l||!t.assembly)return;g(void 0),L(!0);let e=r==="RgfaTabixAdapter"?await J(l,v(t).pluginManager):void 0;if(L(!1),!(!P(t)||!t.assembly))try{let p=b.trim();w({model:t,session:y,conf:K({choice:r,loc:l,indexLoc:k,readsLoc:m?T:void 0,manifest:e,assembly:t.assembly,sample:C,haplotypes:u?q(R):void 0,trackId:x({name:p}),name:p})})}catch(p){g(p)}}return f(O,{className:i.paper,children:[S?a(E,{error:S}):null,f(N,{children:[a(_,{children:"File type"}),a(z,{value:r,onChange:e=>{U(e.target.value),G(void 0),g(void 0)},children:re.map(e=>a(W,{value:e,control:a(j,{}),label:D[e]},e))})]}),a(c,{location:l,name:V[r],rootModel:d,setLocation:Y}),a(c,{location:k,name:X[r],rootModel:d,setLocation:G}),m?a(c,{location:T,name:"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)",rootModel:d,setLocation:Z}):null,a(h,{className:i.field,value:C,onChange:e=>{$(e.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:m?"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample":u?"Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz":"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),u?a(h,{className:i.field,value:R,onChange:e=>{ee(e.target.value)},label:"Haplotypes",slotProps:{htmlInput:{"data-testid":"graph-haplotypes-input"}},helperText:"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file",placeholder:"HG002, HG00733",fullWidth:!0}):null,a(h,{className:i.field,value:b,label:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:e=>{ae(e.target.value)}}),a(H,{session:y,helperText:"Select assembly to add track to",selected:t.assembly,onChange:e=>{t.setAssembly(e)},fullWidth:!0}),a(B,{variant:"contained",className:i.submit,disabled:!l||!b.trim()||!t.assembly||F,onClick:()=>{te()},children:F?"Reading graph.json\u2026":"Submit"})]})}),ye=ne;export{ye as default};
+//# sourceMappingURL=AddTrackWorkflow-JAIB6H2T.js.map

package/dist/chunks/chunk-ZEE3HTOT.js

@@ -0,0 +1,2 @@
+import{c as y}from"./chunk-3VGXCEMQ.js";import{a as p,b as f,c as x,d as A,h as a,i as g,j as d}from"./chunk-6VNDP3UB.js";import{a as T}from"./chunk-OGQ6OQDN.js";var z=5e3;function G(e){return typeof e=="string"&&/^[\w+-][\w.+-]*$/.test(e)}function F(e){return e==null}function M(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function L(e){return M(e)&&G(e.prefix)&&typeof e.foldBelowBp=="number"&&Number.isFinite(e.foldBelowBp)&&e.foldBelowBp>0}function P(e){let n;try{n=JSON.parse(e)}catch{return}if(!M(n)||n.schema!==1)return;let{reference:t,tier:i,index:r,contig:o,bubbles:s,alleles:l}=n;if((F(t)||typeof t=="string"&&t.trim()!=="")&&(F(i)||L(i))&&[r,o,s,l].every(k=>F(k)||G(k)))return{...typeof t=="string"?{reference:t.trim()}:{},...L(i)?{tier:{prefix:i.prefix,foldBelowBp:i.foldBelowBp,...i.format===2?{format:2}:{}}}:{}}}function u(e,n){return d(e,t=>t.replace(/[^/\\]*$/,n))}function R(e){let n=a(e);return[p,f].find(t=>n.endsWith(t))}function N(e){return g(e)&&R(e)!==void 0}function B(e,n){let t=R(e)??p;return d(e,i=>`${i.slice(0,-t.length)}${n}`)}function _(e){return N(e)?B(e,".graph.json"):void 0}async function X(e,n){let t=_(e);if(t)try{let i=await T(t,n).readFile({encoding:"utf8",signal:AbortSignal.timeout(z)});return P(i)}catch{return}}var J={RgfaTabixAdapter:"Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)",RgfaTabixWalks:"Haplotype walks (.walks.bed.gz)",GbzBaseSyntenyAdapter:"GBZ database (.gbz.db)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},K={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz",RgfaTabixWalks:"Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)",GbzBaseSyntenyAdapter:"Path to the .gbz.db written by gbz-base construct",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble)"},w="Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",Z={RgfaTabixAdapter:w,RgfaTabixWalks:w,GbzBaseSyntenyAdapter:"Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)",MinigraphBubbleAdapter:w};function h(e,n){return d(e,t=>t+n)}function C(e){if(!a(e).endsWith(p))throw new Error(`Expected a segments BED ending in ${p}, got ${a(e)}`);return B(e,".links.bed.gz")}function b(e,n){return n?{location:n,indexType:y(a(n),"CSI","TBI")}:{location:h(e,".tbi"),indexType:"TBI"}}function c(e,n){return n!==void 0&&y(a(n),"CSI","TBI")==="CSI"?{location:h(e,".csi"),indexType:"CSI"}:{location:h(e,".tbi"),indexType:"TBI"}}function S(e,n){let t=n.trim();return t&&e?{assemblyNameToPanSN:{[e]:t}}:{}}function E(e,n,t){if(!t)return{};if(t.format===2){let o=u(e,`${t.prefix}${f}`);return{coarse:{foldBelowBp:t.foldBelowBp,graphLocation:o,graphIndex:c(o,n)}}}let i=u(e,`${t.prefix}${p}`),r=u(e,`${t.prefix}.links.bed.gz`);return{coarse:{foldBelowBp:t.foldBelowBp,segmentsLocation:i,segmentsIndex:c(i,n),linksLocation:r,linksIndex:c(r,n)}}}function I(e,n,t){let i=t===e?void 0:t;return S(e,n.trim()||i||"")}function $(e){return e?{readsLocation:e,...a(e).endsWith(".gz")&&g(e)?{readsIndex:{location:h(e,".tbi")}}:{}}:{}}function q(e){return e.split(/[\s,]+/).filter(n=>n!=="")}function W({choice:e,loc:n,indexLoc:t,readsLoc:i,manifest:r,assembly:o,sample:s,haplotypes:l=[]}){if(e==="RgfaTabixWalks"){if(!a(n).endsWith(x))throw new Error(`Expected a walk file ending in ${x}, got ${a(n)}`);return{type:"RgfaTabixAdapter",walksLocation:n,walksIndex:b(n,t),...I(o,s,A(n)),...l.length>0?{defaultHaplotypes:l}:{}}}if(e==="GbzBaseSyntenyAdapter")return{type:"GbzBaseSyntenyAdapter",gbzDbLocation:n,...t?{haplotypeIndexLocation:t}:{},...$(i),...S(o,s)};if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:n,index:b(n,t),...S(o,s)};if(a(n).endsWith(f))return{type:"RgfaTabixAdapter",graphLocation:n,graphIndex:b(n,t),...I(o,s,r?.reference),...E(n,t,r?.tier)};let m=C(n);return{type:"RgfaTabixAdapter",segmentsLocation:n,segmentsIndex:b(n,t),linksLocation:m,linksIndex:c(m,t),...I(o,s,r?.reference),...E(n,t,r?.tier)}}function Q(e){let{choice:n,assembly:t,trackId:i,name:r}=e;return{type:n==="MinigraphBubbleAdapter"?"FeatureTrack":"GraphTrack",trackId:i,name:r,assemblyNames:[t],adapter:W(e),...n==="RgfaTabixAdapter"||n==="RgfaTabixWalks"?{displayDefaults:{labels:{name:{show:!1},description:{show:!1}}}}:{}}}export{N as a,X as b,J as c,K as d,Z as e,q as f,W as g,Q as h};
+//# sourceMappingURL=chunk-ZEE3HTOT.js.map

package/dist/chunks/chunk-ZEE3HTOT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphAddTrackWorkflow/graphManifest.ts", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
+  "sourcesContent": ["import { openLocation } from '@jbrowse/core/util/io'\n\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n} from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// The part of `<prefix>.graph.json`, written by `gfa-to-tabix build`, that\n// Open track reads\nexport interface GraphManifest {\n  reference?: string\n  // `format: 2` when the tier is one `<prefix>.graph.bed.gz`, as gfa-to-tabix\n  // 2 writes it, rather than a segments and links pair\n  tier?: { prefix: string; foldBelowBp: number; format?: 2 }\n}\n\nconst FETCH_TIMEOUT_MS = 5000\n\n// A bare file name beside the manifest: no directory, scheme or leading dot\nfunction isSiblingName(name: unknown): name is string {\n  return typeof name === 'string' && /^[\\w+-][\\w.+-]*$/.test(name)\n}\n\nfunction isAbsent(value: unknown) {\n  return value === undefined || value === null\n}\n\nfunction isPlainRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nfunction isTier(tier: unknown): tier is NonNullable<GraphManifest['tier']> {\n  return (\n    isPlainRecord(tier) &&\n    isSiblingName(tier.prefix) &&\n    typeof tier.foldBelowBp === 'number' &&\n    Number.isFinite(tier.foldBelowBp) &&\n    tier.foldBelowBp > 0\n  )\n}\n\nexport function parseGraphManifest(text: string): GraphManifest | undefined {\n  let json: unknown\n  try {\n    json = JSON.parse(text)\n  } catch {\n    return undefined\n  }\n  if (!isPlainRecord(json) || json.schema !== 1) {\n    return undefined\n  }\n  const { reference, tier, index, contig, bubbles, alleles } = json\n  const valid =\n    (isAbsent(reference) ||\n      (typeof reference === 'string' && reference.trim() !== '')) &&\n    (isAbsent(tier) || isTier(tier)) &&\n    [index, contig, bubbles, alleles].every(\n      f => isAbsent(f) || isSiblingName(f),\n    )\n  if (!valid) {\n    return undefined\n  }\n  return {\n    ...(typeof reference === 'string' ? { reference: reference.trim() } : {}),\n    ...(isTier(tier)\n      ? {\n          tier: {\n            prefix: tier.prefix,\n            foldBelowBp: tier.foldBelowBp,\n            ...(tier.format === 2 ? { format: 2 as const } : {}),\n          },\n        }\n      : {}),\n  }\n}\n\n// A file the manifest names, in the directory of the segments file opened\nexport function besideSegments(segs: FileLocation, fileName: string) {\n  return renamed(segs, name => name.replace(/[^/\\\\]*$/, fileName))\n}\n\n// The suffix of a gfa-to-tabix index file: format 1's segments BED or format\n// 2's graph BED\nfunction indexSuffix(loc: FileLocation) {\n  const name = locationName(loc)\n  return [SEGMENTS_SUFFIX, GRAPH_SUFFIX].find(suffix => name.endsWith(suffix))\n}\n\n// A segments BED, or format 2's graph BED, the rest of the index and the\n// manifest can be found beside\nexport function isGraphIndexLocation(loc: FileLocation) {\n  return readsSiblings(loc) && indexSuffix(loc) !== undefined\n}\n\n// `<prefix><suffix>` beside `<prefix>.segs.bed.gz` or `<prefix>.graph.bed.gz`\nexport function segmentsSibling(segs: FileLocation, suffix: string) {\n  const own = indexSuffix(segs) ?? SEGMENTS_SUFFIX\n  return renamed(segs, name => `${name.slice(0, -own.length)}${suffix}`)\n}\n\nexport function manifestLocation(segs: FileLocation) {\n  return isGraphIndexLocation(segs)\n    ? segmentsSibling(segs, '.graph.json')\n    : undefined\n}\n\n// Undefined for a manifest that is missing, unreadable or not schema 1, so\n// Open track falls back to the files beside the segments alone\nexport async function readGraphManifest(\n  segs: FileLocation,\n  pluginManager?: PluginManager,\n) {\n  const loc = manifestLocation(segs)\n  if (!loc) {\n    return undefined\n  }\n  try {\n    const text = await openLocation(loc, pluginManager).readFile({\n      encoding: 'utf8',\n      signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),\n    })\n    return parseGraphManifest(text)\n  } catch {\n    return undefined\n  }\n}\n", "import { makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport { besideSegments, segmentsSibling } from './graphManifest'\nimport {\n  GRAPH_SUFFIX,\n  SEGMENTS_SUFFIX,\n  WALKS_SUFFIX,\n  locationName,\n  readsSiblings,\n  renamed,\n  walkFileSample,\n} from '../locationName'\n\nimport type { GraphManifest } from './graphManifest'\nimport type { FileLocation } from '@jbrowse/core/util'\n\n// 'RgfaTabixWalks' is an RgfaTabixAdapter read from a walk file\nexport type GraphFileChoice =\n  | 'RgfaTabixAdapter'\n  | 'RgfaTabixWalks'\n  | 'GbzBaseSyntenyAdapter'\n  | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'Indexed GFA (gfa-to-tabix .segs.bed.gz or .graph.bed.gz)',\n  RgfaTabixWalks: 'Haplotype walks (.walks.bed.gz)',\n  GbzBaseSyntenyAdapter: 'GBZ database (.gbz.db)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    \"Path to segments BED (.segs.bed.gz from gfa-to-tabix; the .links.bed.gz, its index and any .graph.json are read beside it), or format 2's .graph.bed.gz\",\n  RgfaTabixWalks:\n    'Path to a walk file (<prefix>.<sample>.walks.bed.gz from gfa-to-tabix --walks, for the sample this assembly is)',\n  GbzBaseSyntenyAdapter: 'Path to the .gbz.db written by gbz-base construct',\n  MinigraphBubbleAdapter: 'Path to bubbles BED (.bed.gz from gfatools bubble)',\n}\n\nconst TABIX_INDEX_FIELD =\n  'Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)'\n\nexport const GRAPH_INDEX_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: TABIX_INDEX_FIELD,\n  RgfaTabixWalks: TABIX_INDEX_FIELD,\n  GbzBaseSyntenyAdapter:\n    'Path to the haplotype index (optional; graph.haplotype-index.db beside the database is assumed)',\n  MinigraphBubbleAdapter: TABIX_INDEX_FIELD,\n}\n\nfunction sibling(loc: FileLocation, suffix: string) {\n  return renamed(loc, name => name + suffix)\n}\n\nfunction linksLocation(loc: FileLocation) {\n  if (!locationName(loc).endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${locationName(loc)}`,\n    )\n  }\n  return segmentsSibling(loc, '.links.bed.gz')\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi =\n    indexLoc !== undefined &&\n    makeIndexType(locationName(indexLoc), 'CSI', 'TBI') === 'CSI'\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// none for a guessed config, which knows no assembly yet; see withWalkReference\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name && assembly ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nfunction coarseTier(\n  loc: FileLocation,\n  indexLoc: FileLocation | undefined,\n  tier: GraphManifest['tier'],\n) {\n  if (!tier) {\n    return {}\n  }\n  if (tier.format === 2) {\n    const graph = besideSegments(loc, `${tier.prefix}${GRAPH_SUFFIX}`)\n    return {\n      coarse: {\n        foldBelowBp: tier.foldBelowBp,\n        graphLocation: graph,\n        graphIndex: siblingIndex(graph, indexLoc),\n      },\n    }\n  }\n  const segs = besideSegments(loc, `${tier.prefix}${SEGMENTS_SUFFIX}`)\n  const links = besideSegments(loc, `${tier.prefix}.links.bed.gz`)\n  return {\n    coarse: {\n      foldBelowBp: tier.foldBelowBp,\n      segmentsLocation: segs,\n      segmentsIndex: siblingIndex(segs, indexLoc),\n      linksLocation: links,\n      linksIndex: siblingIndex(links, indexLoc),\n    },\n  }\n}\n\n// The user's sample wins; the reference the graph's files name (a manifest's,\n// or a walk file's own) stands in when blank\nfunction referencePanSN(\n  assembly: string,\n  sample: string,\n  reference: string | undefined,\n) {\n  const fromManifest = reference === assembly ? undefined : reference\n  return panSN(assembly, sample.trim() || fromManifest || '')\n}\n\n// a bgzipped GAF is read by its tabix index, a plain one whole\nfunction readsConfig(readsLoc: FileLocation | undefined) {\n  return readsLoc\n    ? {\n        readsLocation: readsLoc,\n        ...(locationName(readsLoc).endsWith('.gz') && readsSiblings(readsLoc)\n          ? { readsIndex: { location: sibling(readsLoc, '.tbi') } }\n          : {}),\n      }\n    : {}\n}\n\n// Names typed as a list, by comma or space\nexport function parseHaplotypes(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  readsLoc,\n  manifest,\n  assembly,\n  sample,\n  haplotypes = [],\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  // a GBZ track's GAF reads, which no other choice takes\n  readsLoc?: FileLocation\n  // the `.graph.json` beside an rGFA segments file\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  // a walk file's haplotypes to cut for until the user picks others\n  haplotypes?: string[]\n}) {\n  if (choice === 'RgfaTabixWalks') {\n    if (!locationName(loc).endsWith(WALKS_SUFFIX)) {\n      throw new Error(\n        `Expected a walk file ending in ${WALKS_SUFFIX}, got ${locationName(loc)}`,\n      )\n    }\n    return {\n      type: 'RgfaTabixAdapter',\n      walksLocation: loc,\n      walksIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, walkFileSample(loc)),\n      ...(haplotypes.length > 0 ? { defaultHaplotypes: haplotypes } : {}),\n    }\n  }\n  if (choice === 'GbzBaseSyntenyAdapter') {\n    return {\n      type: 'GbzBaseSyntenyAdapter',\n      gbzDbLocation: loc,\n      ...(indexLoc ? { haplotypeIndexLocation: indexLoc } : {}),\n      ...readsConfig(readsLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  if (locationName(loc).endsWith(GRAPH_SUFFIX)) {\n    return {\n      type: 'RgfaTabixAdapter',\n      graphLocation: loc,\n      graphIndex: tabixIndex(loc, indexLoc),\n      ...referencePanSN(assembly, sample, manifest?.reference),\n      ...coarseTier(loc, indexLoc, manifest?.tier),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...referencePanSN(assembly, sample, manifest?.reference),\n    ...coarseTier(loc, indexLoc, manifest?.tier),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  readsLoc?: FileLocation\n  manifest?: GraphManifest\n  assembly: string\n  sample: string\n  haplotypes?: string[]\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: choice === 'MinigraphBubbleAdapter' ? 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+}

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

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dt=ya.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ie(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&sr(o),n=x(e);return r===void 0?void 0:dr(Ee(n,r),Ee(n,t.assemblyName))},cutChangedFrom(t){return e.cutsWholeWalks!==e.cutsWholeWalksIn(t)||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));var fa={scale:["scale","type"],domain:["scale","domain"],range:["scale","range"],labels:["scale","names"],scheme:["scale","scheme"],reverse:["scale","reverse"],domainMin:["scale","domainMin"],domainMax:["scale","domainMax"],domainMid:["scale","domainMid"],domainQuantile:["scale","domainQuantile"],unknown:["scale","unknown"],title:["legend","title"],descending:["legend","descending"]};function Gi(e){return Object.entries(e).some(([t,o])=>t in fa&&!(t==="scale"&&I(o)))}function Qt(e){if(typeof e=="string")return{value:e};if(!I(e)||!Gi(e))return e;let t={},o={scale:{},legend:{}};for(let[r,n]of Object.entries(e)){let a=fa[r];!a||r==="scale"&&I(n)?t[r]=n:n!==void 0&&(o[a[0]][a[1]]=r==="scale"&&n==="categorical"?"ordinal":n)}for(let r of["scale","legend"])if(Object.keys(o[r]).length>0){let n=t[r];t[r]={...o[r],...I(n)?n:{}}}return t}var wa={color:e=>({encoding:{color:Qt(e)}})};function Zt(){return M.compose("GraphGenomeView",On,dt,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:Lt(Ue),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:Lt(ve)})).preProcessSnapshot(e=>e.color===void 0?e:{...e,color:Qt(e.color)}).views(e=>({get grammar(){return{layoutMode:e.layoutMode,encoding:{color:e.color},size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar({encoding:t,...o}){Object.assign(e,t?{...o,color:t.color}:o)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(de(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${pe(a)}) \u2014 zoom in to view graph (max ${pe(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===de(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=x(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Pt(n,r)):void 0):o(r&&Pt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),V(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(de(t)))},afterAttach(){e.graph||e.load(),L(e,C(()=>e.walkStrip,t=>{e.loadedTrackId&&e.cutsWholeWalks!==e.cutsWholeWalksIn(e.chosenLayoutMode,!t)&&e.load()}))}}))}var Li=Wn()({});function eo(e){e.addViewType(()=>new jn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Zt(),launchKeys:Li,ReactComponent:oe(()=>import("./chunks/GraphGenomeView-2AKRM74B.js"))}))}var to=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function vi(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...to.map(n=>r(o(n)))].filter(n=>n!==void 0)}function oo(e){e.addTrackType(()=>{let t=O("GraphTrack",{},{baseConfiguration:Fn(e),explicitIdentifier:"trackId"}),o=new En({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:Nn(e,"GraphTrack",t)});for(let r of vi(e))o.addDisplayType(r);return o})}function ro(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var ct=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var ka=ct&&ct.__esModule?ct.default:ct;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],Ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ma=Ai("trackHeightConfigSchemaFields"),Lm=be&&be.__esModule?be.default:be;function Sa(){return O("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",Ue),defaultValue:"auto"},encoding:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",ve),defaultValue:"nodes"},...Ma({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId",retired:wa})}var ye=JBrowseExports["@jbrowse/core/svg/svgReady"],Pi=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var xa=Pi("computeSvgReady");var Nm=ye&&ye.__esModule?ye.default:ye;var ut=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var Ra=ut&&ut.__esModule?ut.default:ut;var fe=JBrowseExports["@jbrowse/display-kit/plotMenu"],Ci=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ta=Ci("editPlotMenuItems");var jm=fe&&fe.__esModule?fe.default:fe;var we=JBrowseExports["@jbrowse/render-core/displayPhase"],Ga=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),La=Ga("computeActivityPhase"),va=Ga("computeDisplayPhase");var Om=we&&we.__esModule?we.default:we;function no(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var Bi=new Set(["scale","translateX","translateY"]);function Ii(e){return Object.fromEntries(Object.keys(Cr.properties).filter(t=>!Bi.has(t)).map(t=>[t,e[t]]))}var ao=10;function Ei(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/ao:void 0}var Fi=oe(()=>import("./chunks/GraphTrackSettingsDialog-7XRZQW6T.js"));function Aa(e){return M.compose("LinearGraphDisplay",Bn,Ra(),dt,M.model({type:M.literal("LinearGraphDisplay"),configuration:Ho(e),layoutEngine:nr(Zo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:te(t,"layoutMode"),encoding:te(t,"encoding"),size:te(t,"size"),layers:te(t,"layers"),facet:te(t,"facet"),rows:te(t,"rows"),hover:te(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ie(o))??(r&&vt(r))},get coarseAboveBpPerPx(){return Ei(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=ao*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${pe(o.end-o.start)}, max ${pe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return xa({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return va({renderError:t.renderError,regionTooLarge:t.regionTooLarge,error:t.error},()=>La({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},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))jo(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(ao*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=un(o,t.capFor(r),Q(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=Q(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||no(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&mn(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{V(t)&&t.recuts===a&&xt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Te(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||Q(o).cutMargins!==Q(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});V(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&ar(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),L(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;L(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-Qe)?.total??0)+Qe;(t.facetGrid?.total??0)+Qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Te(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Te(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||no(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end),{encoding:i,...s}=t.grammar;return{...Ii(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...s,color:i?.color,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!ir(o))return[];let n=Ie(o),a=vt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[Fi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-E5Q7MLCH.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();pt(o,{label:"Graph genome view",icon:tt,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!xt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:xn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:Rn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...Ta(t)]}}))}function io(e){e.addDisplayType(()=>{let t=Sa();return Object.assign(new ka({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Aa(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-WWQ73BO5.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Ni(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Se(t,o,r)}:e}var Hi=O("MinigraphBubbleAdapter",{bubblesLocation:B("/path/to/graph.bb.bed.gz"),index:j("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Ni}),Pa=Hi;function so(e){e.addAdapterType(()=>new Z({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED 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ji=O("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:B("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:j("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.tier.links.bed.gz"),linksIndex:j("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:j("RgfaCoarseGraphIndex")}),Wi=O("RgfaTabixAdapter",{segmentsLocation:B("/path/to/graph.segs.bed.gz"),segmentsIndex:j("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.links.bed.gz"),linksIndex:j("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:j("RgfaGraphIndex"),walksLocation:B(""),walksIndex:j("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ji},{explicitlyTyped:!0,preProcessSnapshot:Vi}),Ba=Wi;function po(e){e.addAdapterType(()=>new Z({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Ba,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-CEGFN2QY.js").then(t=>t.default)}))}var Oi=["LinearMultiSampleVariantDisplay"],Di=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function _i(e,t){return e?`Pinned to ${Ze(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function zi(e,t){let o=x(e),r=t.flatMap(n=>n?[Ln(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function $i(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return Vo(t.parentTrack.configuration,"adapter")},get walkForms(){return this.configuredAdapter.type==="WalkFormsAdapter"}})).views(t=>({get adapterConfig(){let o=t.configuredAdapter;return t.walkForms?{...o,...t.formsPinned?{pinned:t.formsPinned}:{},...t.formsFloorBp===void 0?{}:{floorBp:t.formsFloorBp}}:o},get formsWindow(){return Tn(this.adapterConfig.pinned)},get formsFloor(){return Gn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=Ao(t),r=cn(o)?Te(o):void 0;return r&&r.end>r.start?{refName:r.refName,start:Math.max(0,Math.floor(r.start)),end:Math.ceil(r.end)}:void 0}})).volatile(()=>({warnedWindow:void 0})).actions(t=>{let{setSources:o}=t,r=()=>{zi(t,[t.warnedWindow,t.formsWindow])};return{setFormsPinned(n){r(),t.formsPinned=n},setFormsFloorBp(n){r(),t.formsFloorBp=n},setSources(n,a){t.walkForms&&(r(),t.warnedWindow=t.formsWindow),o?.(n,a)}}}).views(t=>{let{trackMenuItems:o}=t;return{formsMenuItems(){let r=t.formsWindow,n=t.visibleWindow;return[{label:_i(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the forms from the region the view shows. Panning and zooming leave the forms alone",disabled:!n||r!==void 0&&Ze(n)===Ze(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Di.map(({label:a,value:i})=>({label:a,type:"radio",checked:t.formsFloor===i,onClick:()=>{t.setFormsFloorBp(i)}}))}]},trackMenuItems(){return t.walkForms?[...o(),...this.formsMenuItems()]:o()}}})}function co(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Oi.includes(t.name)&&t.extendStateModel($i),t))}var Ji=O("WalkFormsAdapter",{walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:j("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:vn},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:xe}),Ia=Ji;function uo(e){e.addAdapterType(()=>new Z({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:Ia,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-LTAKACZD.js").then(t=>t.default)}))}var Yi=O("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:j("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:B(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:xe}),Ea=Yi;function mo(e){e.addAdapterType(()=>new Z({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:Ea,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-B6V3YNW7.js").then(t=>t.default)}))}var Ui=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Xi(e){return ft(e).toLowerCase().endsWith(".gbz.db")}function qi(e){let t=e.adapter;return t?.type!==void 0&&ln.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ki(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Oo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Qi(e,t,o){let r=n=>Qo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Xi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Ko(e))return r("RgfaTabixAdapter");if(ft(e).endsWith(Wo)&&(t!==void 0||zo(e)))return r("RgfaTabixWalks")}}function lo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",qi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ki),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Qi(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Ui.has(o)?"GraphTrack":t(o,r))}function go(e){let t;if(I(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Zi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Fa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Na(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>I(o)&&Array.isArray(o.displays)?o.displays.filter(r=>I(r)&&r.type==="LinearGraphDisplay"):[])}function Ha(e,t,o){let r=[],n=Re(e),a=new Set(n.map(i=>I(i)?i.id:void 0));for(let i of n){if(I(i)&&i.id===t)for(let s of Na(i)){let p=go(s.hoverHighlight);p&&Fa(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of I(i)?[...Na(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((c,m)=>{let S=go(c);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(I(i)&&i.type==="GraphGenomeView"&&Zi(i,t,a)){let s=go(i.hoverHighlight);s&&Fa(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var es=Sn()(e=>({highlight:{height:"100%",position:"absolute",background:Je(e.palette.primary.main,.08),borderLeft:`1px solid ${Je(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Je(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),ts=St(function({model:t,region:o}){let{classes:r}=es(),n=t.getHighlightCoords(o);return n?F("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),os=St(function({model:t}){let{views:o}=x(t);return F(Io,{children:Ha([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>F(ts,{model:t,region:n},`graph-hover-${r}`))})}),Va=os;var rs="LinearGenomeView-TracksContainerComponent";function ho(e){e.contributeToExtensionPoint(rs,({model:t})=>F(Va,{model:t},"graphgenomeview-hover-highlight"))}function ns(e){return e.views(t=>({get adapterConfig(){return gn(t,t.parentTrack.configuration)}}))}function bo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&to.includes(t.name)&&t.extendStateModel(ns),t))}var ja="GraphGenomeView";var Wa="8.2.0";var yo=class extends An{constructor(){super(...arguments);this.name=ja;this.version=Wa}install(o){eo(o),io(o),oo(o),ro(o),ho(o),po(o),so(o),Wt(o),mo(o),uo(o),co(o),Dt(o),lo(o),bo(o),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o)),o.addRpcMethod(()=>new Ve(o))}configure(o){try{Po(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:tt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{yo as default};
+`);return[{type:"radio",label:"Every sample",checked:o===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:r(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:o!==void 0&&!r(t),onClick:()=>{x(e).queueDialog(n=>[Sr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return ee([{value:void 0,label:"None"},...e.walkRowGroupFields.map(o=>({value:o,label:o}))],t,o=>{e.setWalkRowGroupBy(o===void 0?void 0:{field:o})})},tubeMapPanelMenuItems(){let{graph:t,walkRowSampleTable:o}=e,{field:r}=e.facetSetting,n=r===""?e.walkRowGroupBy?.field:void 0,a=i=>!!t&&qe(t,i).length>1;return[...ee(tn.map(i=>({value:i.field,label:i.label,disabled:i.field!==""&&!a({by:i.field})})),n?void 0:r,i=>{e.setFacet(i),i===""&&e.setWalkRowGroupBy(void 0)}),...ee(e.walkRowGroupFields.map(i=>({value:i,label:`By 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rows",checked:e.walkRibbons,onClick:()=>{e.setLayer("walkRibbons",!e.walkRibbons)}},{type:"checkbox",label:"Letter shared blocks",checked:e.layerSet.has("walkBlocks"),onClick:()=>{e.setLayer("walkBlocks",!e.layerSet.has("walkBlocks"))}},{type:"checkbox",label:"Order rows by shared sequence",checked:e.walkRowOrder==="shared",onClick:()=>{e.setWalkRowOrder(e.walkRowOrder==="shared"?void 0:"shared")}}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:ee(ve.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:zn,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&ha(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>Tr;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{x(e).queueDialog(a=>[xr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{x(e).queueDialog(a=>[Rr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...ee(hr.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Ct.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=Q(e.chosenLayoutMode),r=ba.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${Kt(o)}${o.value==="force"?` (${r})`:""}`,icon:Dn,subMenu:[...rr.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?ba.map(([i,s])=>({...a,label:`${Kt(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:Kt(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:_n,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:ee(Ct.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show",icon:br,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of Mn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))pt(t,n);return t}}));var dt=ya.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ie(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&sr(o),n=x(e);return r===void 0?void 0:dr(Ee(n,r),Ee(n,t.assemblyName))},cutChangedFrom(t){return e.cutsWholeWalks!==e.cutsWholeWalksIn(t)||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));var fa={scale:["scale","type"],domain:["scale","domain"],range:["scale","range"],labels:["scale","names"],scheme:["scale","scheme"],reverse:["scale","reverse"],domainMin:["scale","domainMin"],domainMax:["scale","domainMax"],domainMid:["scale","domainMid"],domainQuantile:["scale","domainQuantile"],unknown:["scale","unknown"],title:["legend","title"],descending:["legend","descending"]};function Gi(e){return Object.entries(e).some(([t,o])=>t in fa&&!(t==="scale"&&I(o)))}function Qt(e){if(typeof e=="string")return{value:e};if(!I(e)||!Gi(e))return e;let t={},o={scale:{},legend:{}};for(let[r,n]of Object.entries(e)){let a=fa[r];!a||r==="scale"&&I(n)?t[r]=n:n!==void 0&&(o[a[0]][a[1]]=r==="scale"&&n==="categorical"?"ordinal":n)}for(let r of["scale","legend"])if(Object.keys(o[r]).length>0){let n=t[r];t[r]={...o[r],...I(n)?n:{}}}return t}var wa={color:e=>({encoding:{color:Qt(e)}})};function Zt(){return M.compose("GraphGenomeView",On,dt,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:Lt(Ue),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:Lt(ve)})).preProcessSnapshot(e=>e.color===void 0?e:{...e,color:Qt(e.color)}).views(e=>({get grammar(){return{layoutMode:e.layoutMode,encoding:{color:e.color},size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar({encoding:t,...o}){Object.assign(e,t?{...o,color:t.color}:o)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(de(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${pe(a)}) \u2014 zoom in to view graph (max ${pe(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===de(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=x(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Pt(n,r)):void 0):o(r&&Pt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),V(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(de(t)))},afterAttach(){e.graph||e.load(),L(e,C(()=>e.walkStrip,t=>{e.loadedTrackId&&e.cutsWholeWalks!==e.cutsWholeWalksIn(e.chosenLayoutMode,!t)&&e.load()}))}}))}var Li=Wn()({});function eo(e){e.addViewType(()=>new jn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Zt(),launchKeys:Li,ReactComponent:oe(()=>import("./chunks/GraphGenomeView-2AKRM74B.js"))}))}var to=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function vi(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...to.map(n=>r(o(n)))].filter(n=>n!==void 0)}function oo(e){e.addTrackType(()=>{let t=O("GraphTrack",{},{baseConfiguration:Fn(e),explicitIdentifier:"trackId"}),o=new En({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:Nn(e,"GraphTrack",t)});for(let r of vi(e))o.addDisplayType(r);return o})}function ro(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var ct=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var ka=ct&&ct.__esModule?ct.default:ct;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],Ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ma=Ai("trackHeightConfigSchemaFields"),Lm=be&&be.__esModule?be.default:be;function Sa(){return O("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",Ue),defaultValue:"auto"},encoding:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",ve),defaultValue:"nodes"},...Ma({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId",retired:wa})}var ye=JBrowseExports["@jbrowse/core/svg/svgReady"],Pi=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var xa=Pi("computeSvgReady");var Nm=ye&&ye.__esModule?ye.default:ye;var ut=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var Ra=ut&&ut.__esModule?ut.default:ut;var fe=JBrowseExports["@jbrowse/display-kit/plotMenu"],Ci=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ta=Ci("editPlotMenuItems");var jm=fe&&fe.__esModule?fe.default:fe;var we=JBrowseExports["@jbrowse/render-core/displayPhase"],Ga=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),La=Ga("computeActivityPhase"),va=Ga("computeDisplayPhase");var Om=we&&we.__esModule?we.default:we;function no(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var Bi=new Set(["scale","translateX","translateY"]);function Ii(e){return Object.fromEntries(Object.keys(Cr.properties).filter(t=>!Bi.has(t)).map(t=>[t,e[t]]))}var ao=10;function Ei(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/ao:void 0}var Fi=oe(()=>import("./chunks/GraphTrackSettingsDialog-7XRZQW6T.js"));function Aa(e){return M.compose("LinearGraphDisplay",Bn,Ra(),dt,M.model({type:M.literal("LinearGraphDisplay"),configuration:Ho(e),layoutEngine:nr(Zo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:te(t,"layoutMode"),encoding:te(t,"encoding"),size:te(t,"size"),layers:te(t,"layers"),facet:te(t,"facet"),rows:te(t,"rows"),hover:te(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ie(o))??(r&&vt(r))},get coarseAboveBpPerPx(){return Ei(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=ao*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${pe(o.end-o.start)}, max ${pe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return xa({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return va({renderError:t.renderError,regionTooLarge:t.regionTooLarge,error:t.error},()=>La({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},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))jo(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(ao*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=un(o,t.capFor(r),Q(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=Q(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||no(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&mn(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{V(t)&&t.recuts===a&&xt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Te(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||Q(o).cutMargins!==Q(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});V(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&ar(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),L(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),L(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;L(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),L(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-Qe)?.total??0)+Qe;(t.facetGrid?.total??0)+Qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),L(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Te(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Te(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||no(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end),{encoding:i,...s}=t.grammar;return{...Ii(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...s,color:i?.color,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!ir(o))return[];let n=Ie(o),a=vt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=c=>{t.setSubgraphHaplotypes(c),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[Fi,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-E5Q7MLCH.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();pt(o,{label:"Graph genome view",icon:tt,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!xt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:xn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:Rn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...Ta(t)]}}))}function io(e){e.addDisplayType(()=>{let t=Sa();return Object.assign(new ka({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:Aa(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-WWQ73BO5.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Ni(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Se(t,o,r)}:e}var Hi=O("MinigraphBubbleAdapter",{bubblesLocation:B("/path/to/graph.bb.bed.gz"),index:j("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Ni}),Pa=Hi;function so(e){e.addAdapterType(()=>new Z({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:Pa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-4OOBJ44C.js").then(t=>t.default)}))}function Ca(e){let{uri:t,baseUri:o,csi:r,format:n}=e;return typeof t!="string"?e:n===2?{...e,graphLocation:{uri:`${t}${yt}`,baseUri:o},graphIndex:Se(`${t}${yt}`,o,r)}:{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Se(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Se(`${t}.links.bed.gz`,o,r)}}function Vi(e){let{coarse:t,baseUri:o,csi:r}=e;return xe(Ca(typeof t=="object"&&t!==null?{...e,coarse:Ca({baseUri:o,csi:r,...t})}:e))}var ji=O("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:B("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:j("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.tier.links.bed.gz"),linksIndex:j("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:j("RgfaCoarseGraphIndex")}),Wi=O("RgfaTabixAdapter",{segmentsLocation:B("/path/to/graph.segs.bed.gz"),segmentsIndex:j("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:B("/path/to/graph.links.bed.gz"),linksIndex:j("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),graphLocation:B(""),graphIndex:j("RgfaGraphIndex"),walksLocation:B(""),walksIndex:j("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:ji},{explicitlyTyped:!0,preProcessSnapshot:Vi}),Ba=Wi;function po(e){e.addAdapterType(()=>new Z({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Ba,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-CEGFN2QY.js").then(t=>t.default)}))}var Oi=["LinearMultiSampleVariantDisplay"],Di=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function _i(e,t){return e?`Pinned to ${Ze(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function zi(e,t){let o=x(e),r=t.flatMap(n=>n?[Ln(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function $i(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return Vo(t.parentTrack.configuration,"adapter")},get walkForms(){return this.configuredAdapter.type==="WalkFormsAdapter"}})).views(t=>({get adapterConfig(){let o=t.configuredAdapter;return t.walkForms?{...o,...t.formsPinned?{pinned:t.formsPinned}:{},...t.formsFloorBp===void 0?{}:{floorBp:t.formsFloorBp}}:o},get formsWindow(){return Tn(this.adapterConfig.pinned)},get formsFloor(){return Gn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=Ao(t),r=cn(o)?Te(o):void 0;return r&&r.end>r.start?{refName:r.refName,start:Math.max(0,Math.floor(r.start)),end:Math.ceil(r.end)}:void 0}})).volatile(()=>({warnedWindow:void 0})).actions(t=>{let{setSources:o}=t,r=()=>{zi(t,[t.warnedWindow,t.formsWindow])};return{setFormsPinned(n){r(),t.formsPinned=n},setFormsFloorBp(n){r(),t.formsFloorBp=n},setSources(n,a){t.walkForms&&(r(),t.warnedWindow=t.formsWindow),o?.(n,a)}}}).views(t=>{let{trackMenuItems:o}=t;return{formsMenuItems(){let r=t.formsWindow,n=t.visibleWindow;return[{label:_i(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the forms from the region the view shows. Panning and zooming leave the forms alone",disabled:!n||r!==void 0&&Ze(n)===Ze(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Di.map(({label:a,value:i})=>({label:a,type:"radio",checked:t.formsFloor===i,onClick:()=>{t.setFormsFloorBp(i)}}))}]},trackMenuItems(){return t.walkForms?[...o(),...this.formsMenuItems()]:o()}}})}function co(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Oi.includes(t.name)&&t.extendStateModel($i),t))}var Ji=O("WalkFormsAdapter",{walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:j("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:vn},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:xe}),Ia=Ji;function uo(e){e.addAdapterType(()=>new Z({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:Ia,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-LTAKACZD.js").then(t=>t.default)}))}var Yi=O("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:B("/path/to/graph.walks.bed.gz"),walksIndex:j("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:B(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:xe}),Ea=Yi;function mo(e){e.addAdapterType(()=>new Z({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:Ea,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-B6V3YNW7.js").then(t=>t.default)}))}var Ui=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Xi(e){return ft(e).toLowerCase().endsWith(".gbz.db")}function qi(e){let t=e.adapter;return t?.type!==void 0&&ln.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Ki(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Oo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Qi(e,t,o){let r=n=>Qo({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Xi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Ko(e))return r("RgfaTabixAdapter");if(ft(e).endsWith(Wo)&&(t!==void 0||zo(e)))return r("RgfaTabixWalks")}}function lo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",qi),e.addToExtensionPoint("Core-preProcessTrackConfig",Ki),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Qi(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Ui.has(o)?"GraphTrack":t(o,r))}function go(e){let t;if(I(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Zi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Fa(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Na(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>I(o)&&Array.isArray(o.displays)?o.displays.filter(r=>I(r)&&r.type==="LinearGraphDisplay"):[])}function Ha(e,t,o){let r=[],n=Re(e),a=new Set(n.map(i=>I(i)?i.id:void 0));for(let i of n){if(I(i)&&i.id===t)for(let s of Na(i)){let p=go(s.hoverHighlight);p&&Fa(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of I(i)?[...Na(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((c,m)=>{let S=go(c);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(I(i)&&i.type==="GraphGenomeView"&&Zi(i,t,a)){let s=go(i.hoverHighlight);s&&Fa(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var es=Sn()(e=>({highlight:{height:"100%",position:"absolute",background:Je(e.palette.primary.main,.08),borderLeft:`1px solid ${Je(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Je(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),ts=St(function({model:t,region:o}){let{classes:r}=es(),n=t.getHighlightCoords(o);return n?F("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),os=St(function({model:t}){let{views:o}=x(t);return F(Io,{children:Ha([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>F(ts,{model:t,region:n},`graph-hover-${r}`))})}),Va=os;var rs="LinearGenomeView-TracksContainerComponent";function ho(e){e.contributeToExtensionPoint(rs,({model:t})=>F(Va,{model:t},"graphgenomeview-hover-highlight"))}function ns(e){return e.views(t=>({get adapterConfig(){return gn(t,t.parentTrack.configuration)}}))}function bo(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&to.includes(t.name)&&t.extendStateModel(ns),t))}var ja="GraphGenomeView";var Wa="8.3.0";var yo=class extends An{constructor(){super(...arguments);this.name=ja;this.version=Wa}install(o){eo(o),io(o),oo(o),ro(o),ho(o),po(o),so(o),Wt(o),mo(o),uo(o),co(o),Dt(o),lo(o),bo(o),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o)),o.addRpcMethod(()=>new Ve(o))}configure(o){try{Po(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:tt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{yo as default};
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