jbrowse-plugin-graphgenomeviewer 7.4.4 → 7.5.0

package/dist/chunks/GraphTrackSettingsDialog-EVIIGC5G.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
-  "sourcesContent": ["import { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from '../../GraphGenomeView/components/LabelledSelect'\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: '0', label: 'None' },\n  { value: '1', label: '1 hop' },\n  { value: '2', label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const adapter = model.sourceAdapter\n  return adapter?.type === 'RgfaTabixAdapter' && !walkIndexed(adapter) ? (\n    <div className={classes.section}>\n      <LabelledSelect\n        label=\"Graph context\"\n        sx={{ minWidth: 200 }}\n        value={String(model.subgraphContext)}\n        options={SUBGRAPH_CONTEXTS}\n        testId=\"graph-context-select\"\n        onChange={hops => {\n          model.setSubgraphContext(Number(hops))\n          model.recut()\n        }}\n      />\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useRef, useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nfunction parseHaplotypeList(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft)\n    const unchanged =\n      parsed.join('\\n') === (model.cutHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      model.recut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too, on\n// Enter or when the field loses focus. The set applies when the list closes\n// or, with the list closed, as it changes. Not MUI's `autoSelect`: in a\n// multiple select its blur toggles the highlighted option, so a pick made by\n// keyboard was dropped again on Tab.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const draftRef = useRef(draft)\n  const typed = useRef('')\n  const [open, setOpen] = useState(false)\n  const apply = (haplotypes: string[]) => {\n    if (haplotypes.join('\\n') !== (model.cutHaplotypes ?? []).join('\\n')) {\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onInputChange={(_, text) => {\n        typed.current = text\n      }}\n      onClose={(_, reason) => {\n        setOpen(false)\n        const text = typed.current.trim()\n        if (reason === 'blur' && text && !draftRef.current.includes(text)) {\n          draftRef.current = [...draftRef.current, text]\n          setDraft(draftRef.current)\n        }\n        apply(draftRef.current)\n      }}\n      onChange={(_, value) => {\n        draftRef.current = value\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set. The inner field is\n// keyed on it so an outside change (a restored session, a launch) resets the\n// draft rather than fighting it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const key = model.cutHaplotypes?.join(',') ?? ''\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField key={key} model={model} names={names} />\n      ) : (\n        <HaplotypeListField key={key} model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
-  "mappings": "8ZASA,IAAMA,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAWKC,EAAoB,CACxB,CAAE,MAAO,IAAK,MAAO,MAAO,EAC5B,CAAE,MAAO,IAAK,MAAO,OAAQ,EAC7B,CAAE,MAAO,IAAK,MAAO,QAAS,CAChC,EAEMC,EAAwBC,EAAS,SAA+B,CACpE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIN,EAAU,EACxBO,EAAUF,EAAM,cACtB,OAAOE,GAAS,OAAS,oBAAsB,CAACC,EAAYD,CAAO,EACjEE,EAAC,OAAI,UAAWH,EAAQ,QACtB,UAAAI,EAACC,EAAA,CACC,MAAM,gBACN,GAAI,CAAE,SAAU,GAAI,EACpB,MAAO,OAAON,EAAM,eAAe,EACnC,QAASH,EACT,OAAO,uBACP,SAAUU,GAAQ,CAChBP,EAAM,mBAAmB,OAAOO,CAAI,CAAC,EACrCP,EAAM,MAAM,CACd,EACF,EACAK,EAACG,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBAAiB,6KAIrE,GACF,EACE,IACN,CAAC,EAEMC,EAAQX,ECjDf,IAAMY,EAAYC,EAAW,EAAE,CAC7B,QAAS,CACP,aAAc,EAChB,CACF,CAAC,EAED,SAASC,EAAmBC,EAAc,CACxC,OAAOA,EAAK,MAAM,QAAQ,EAAE,OAAOC,GAAQA,IAAS,EAAE,CACxD,CAEA,IAAMC,EAAqBC,EAAS,SAA4B,CAC9D,MAAAC,CACF,EAEG,CACD,GAAM,CAACC,EAAOC,CAAQ,EAAIC,EAASH,EAAM,eAAe,KAAK,IAAI,GAAK,EAAE,EAClEI,EAAQ,IAAM,CAClB,IAAMC,EAASV,EAAmBM,CAAK,EAErCI,EAAO,KAAK;AAAA,CAAI,KAAOL,EAAM,eAAiB,CAAC,GAAG,KAAK;AAAA,CAAI,IAE3DA,EAAM,sBAAsBK,CAAM,EAClCL,EAAM,MAAM,EAEhB,EACA,OACEM,EAACC,EAAA,CACC,UAAS,GACT,MAAM,aACN,YAAY,kBACZ,MAAON,EACP,UAAW,CAAE,UAAW,CAAE,cAAe,wBAAyB,CAAE,EACpE,SAAU,GAAK,CACbC,EAAS,EAAE,OAAO,KAAK,CACzB,EACA,OAAQ,IAAM,CACZE,EAAM,CACR,EACA,UAAW,GAAK,CACV,EAAE,MAAQ,SACZA,EAAM,CAEV,EACF,CAEJ,CAAC,EAQKI,EAAqBT,EAAS,SAA4B,CAC9D,MAAAC,EACA,MAAAS,CACF,EAGG,CACD,GAAM,CAACR,EAAOC,CAAQ,EAAIC,EAASH,EAAM,eAAiB,CAAC,CAAC,EACtDU,EAAWC,EAAOV,CAAK,EACvBW,EAAQD,EAAO,EAAE,EACjB,CAACE,EAAMC,CAAO,EAAIX,EAAS,EAAK,EAChCC,EAASW,GAAyB,CAClCA,EAAW,KAAK;AAAA,CAAI,KAAOf,EAAM,eAAiB,CAAC,GAAG,KAAK;AAAA,CAAI,IACjEA,EAAM,sBAAsBe,CAAU,EACtCf,EAAM,MAAM,EAEhB,EACA,OACEM,EAACU,EAAA,CACC,SAAQ,GACR,SAAQ,GACR,qBAAoB,GACpB,QAASP,EACT,MAAOR,EACP,KAAMY,EACN,OAAQ,IAAM,CACZC,EAAQ,EAAI,CACd,EACA,cAAe,CAACG,EAAGrB,IAAS,CAC1BgB,EAAM,QAAUhB,CAClB,EACA,QAAS,CAACqB,EAAGC,IAAW,CACtBJ,EAAQ,EAAK,EACb,IAAMlB,EAAOgB,EAAM,QAAQ,KAAK,EAC5BM,IAAW,QAAUtB,GAAQ,CAACc,EAAS,QAAQ,SAASd,CAAI,IAC9Dc,EAAS,QAAU,CAAC,GAAGA,EAAS,QAASd,CAAI,EAC7CM,EAASQ,EAAS,OAAO,GAE3BN,EAAMM,EAAS,OAAO,CACxB,EACA,SAAU,CAACO,EAAGE,IAAU,CACtBT,EAAS,QAAUS,EACnBjB,EAASiB,CAAK,EACTN,GACHT,EAAMe,CAAK,CAEf,EACA,YAAaC,GACXd,EAACC,EAAA,CACE,GAAGa,EACJ,MAAM,aACN,YAAanB,EAAM,SAAW,EAAI,kBAAoB,OACtD,UAAW,CACT,GAAGmB,EAAO,UACV,UAAW,CACT,GAAGA,EAAO,UAAU,UACpB,cAAe,wBACjB,CACF,EACF,EAEJ,CAEJ,CAAC,EAKKC,EAA0BtB,EAAS,SAAiC,CACxE,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAsB,CAAQ,EAAI7B,EAAU,EACxBgB,EAAQT,EAAM,eACduB,EAAMvB,EAAM,eAAe,KAAK,GAAG,GAAK,GACxCwB,EAAUxB,EAAM,cACtB,OAAOwB,GAAWC,EAAgBD,CAAO,EACvCE,EAAC,OAAI,UAAWJ,EAAQ,QACrB,UAAAb,EACCH,EAACE,EAAA,CAA6B,MAAOR,EAAO,MAAOS,GAA1Bc,CAAiC,EAE1DjB,EAACR,EAAA,CAA6B,MAAOE,GAAZuB,CAAmB,EAE9CG,EAACC,EAAA,CAAW,QAAQ,UAAU,UAAU,MAAM,MAAM,iBACjD,UAAAlB,EACG,wBAAwBA,EAAM,OAAO,eAAe,CAAC,0DACrD,sHAAuH,IAAI,6BAEjI,GACF,EACE,IACN,CAAC,EAEMmB,EAAQP,ECvJA,SAARQ,EAA0C,CAC/C,MAAAC,EACA,QAAAC,CACF,EAGG,CACD,OACEC,EAACC,EAAA,CAAoB,MAAOH,EAAO,QAASC,EAC1C,UAAAG,EAACC,EAAA,CAAsB,MAAOL,EAAO,EACrCI,EAACE,EAAA,CAAwB,MAAON,EAAO,GACzC,CAEJ",
-  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "jsx", "LabelledSelect", "hops", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "HaplotypeListField", "observer", "model", "draft", "setDraft", "useState", "apply", "parsed", "jsx", "TextField", "HaplotypePickField", "names", "draftRef", "useRef", "typed", "open", "setOpen", "haplotypes", "Autocomplete", "_", "reason", "value", "params", "SubgraphHaplotypesField", "classes", "key", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
-}

package/dist/chunks/LinearGraphDisplay-ZC4BQ27J.js

@@ -1,2 +0,0 @@
-import{a as h}from"./chunk-HCDKP3IP.js";import"./chunk-6VNU7SD4.js";import"./chunk-LE43I4PT.js";import"./chunk-GRTN25B6.js";import"./chunk-7RJMG6I2.js";import"./chunk-WLRRI35A.js";import"./chunk-VZQ6VOUP.js";import"./chunk-2KVE7YAS.js";import"./chunk-S333HOG5.js";import"./chunk-P3FBI5ML.js";import"./chunk-6WUWQX2P.js";import"./chunk-KIYRMZWP.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import"./chunk-IKJZPPOA.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as T}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as e,c as d,d as i}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var f=n&&n.__esModule?n.default:n;var l=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var v=l&&l.__esModule?l.default:l;var p=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=p&&p.__esModule?p.default:p;var c=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var L=c&&c.__esModule?c.default:c;var s=JBrowseExports["@jbrowse/display-ui"],u=r=>s!=null&&r in Object(s)?s[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=u("BottomRightCornerContext");var g=u("TrackOverlayPortal");var C=u("useChromeOverlayOverride");var U=s&&s.__esModule?s.default:s;var k={TooLarge:L,ErrorBar:v,Loading:O,BackgroundProgress:f},m="Zoom in to see features, or force load this track for the rest of the session (may be slow)",M="Force load this track for the rest of the session (may be slow)";function H(r){let o=r.error??r.renderError,t=o instanceof Error&&o.regionTooLarge===!0;return{error:{error:o,onRetry:t?void 0:()=>{r.reload()}},tooLarge:{message:[r.regionTooLargeReason,r.zoomCanReleaseGate?m:M].filter(Boolean).join(". "),onForceLoad:()=>{r.forceLoad()}},loading:{message:r.statusMessage,progress:r.statusProgress,canceled:r.fetchCanceled,onCancel:()=>{r.cancelFetchByUser()},onRetry:()=>{r.reload()}},background:{message:r.statusMessage,progress:r.statusProgress}}}var _=i(function({model:o,phase:t,drawn:x,testid:E,style:B,children:G,...S}){let{TooLarge:b,ErrorBar:P,Loading:A,BackgroundProgress:D}=C()??k,[R,I]=T(null),a=H(o),y={...S,"data-testid":E,"data-display-id":o.configuration.displayId,"data-display-drawn":x,"data-display-phase":t};return t==="tooLarge"?e("div",{style:{display:"contents"},...y,children:e(g,{children:e("div",{style:{pointerEvents:"auto"},children:e(b,{model:o,...a.tooLarge})})})}):d("div",{style:{position:"relative",height:o.height,...B},...y,children:[e(w,{value:R,children:G}),d(g,{children:[t==="error"?e(P,{model:o,visible:!0,...a.error}):null,e(A,{model:o,...a.loading,visible:t==="loading"||t==="canceled",immediate:!x}),e("div",{ref:I,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:t==="ready"&&o.statusMessage?e(D,{model:o,visible:!0,...a.background}):null})]})]})});var j=i(function({model:o}){return e(_,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(h,{model:o,ownChrome:!1})})}),so=j;export{so as default};
-//# sourceMappingURL=LinearGraphDisplay-ZC4BQ27J.js.map

package/dist/chunks/RgfaTabixAdapter-XSOIEWBK.js

@@ -1,2 +0,0 @@
-import{a as b}from"./chunk-OJWBLPPH.js";import"./chunk-QV7SSOMJ.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import{C as m,D as k,E as x,b as g,u as c,v as u,w as h,x as w}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as f}from"./chunk-TENPGIPX.js";var l=class extends g{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let a=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),r=e.length===0&&d(n)?new b(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:s,walks:r,refNames:new x(r?.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,a={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,a,s&&((r,{start:t,end:i})=>s.reader.queryStart(t,{...a,refName:r,end:i})))}async hasDataForRefName(){return!0}getFeatures(e,a={}){return N(async s=>{let n=await this.fine.refNames.resolveMapped(e,a);if(n!==void 0){let{walks:r}=this.fine,t=i=>{s.next(i)};await(r?this.walkFeatures(r,n,e,a,t):this.segmentFeatures(n,e,a,t))}s.complete()},a.signal)}async walkFeatures(e,a,s,n,r){let t=await f("Downloading walks",n.statusCallback,()=>e.referenceNodes(a,s,n));for(let i of t){let o=String(i.id);r(new p({uniqueId:o,refName:s.refName,start:i.start,end:i.end,name:o,type:"segment",rank:0,stableName:i.refName}))}}async segmentFeatures(e,a,s,n){await f("Downloading segments",s.statusCallback,()=>w(this.fine.segments,e,a.start,a.end,{signal:s.signal,lineCallback:r=>{let{segment:t,anchored:i}=c(r);if(i&&t.refName!==e)return;let o=u(t);n(new p({uniqueId:t.id,refName:a.refName,start:t.start,end:t.end,name:t.id,type:"segment",rank:t.rank,stableName:t.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,a={}){let{hops:s,signal:n,tier:r}=a,t=this.index(r),i=await t.refNames.resolve(e,{signal:n});if(i===void 0)throw new Error(k(e));return t.walks?t.walks.subgraph(i,e,a):h(t,{refName:i,start:e.start,end:e.end},{hops:s,signal:n})}};export{l as default};
-//# sourceMappingURL=RgfaTabixAdapter-XSOIEWBK.js.map

package/dist/chunks/RgfaTabixAdapter-XSOIEWBK.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts"],
-  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { parseSegmentRow, rgfaCut, segmentSamples } from '@jbrowse/graph-walks'\n\nimport { locationIsSet } from '../locationName.ts'\nimport {\n  PanSNRefNames,\n  openTabixSlot,\n  unmappedRegionMessage,\n} from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\nimport { WalkIndex } from './walkReader.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { WalkCut } from './walkCut.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkIndex\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine = this.openIndex([])\n  private coarse: GraphIndex | undefined\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches. A walk-indexed graph's walk file names the same sequences,\n  // and it has no segment file.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const walks =\n      under.length === 0 && locationIsSet(walksLocation)\n        ? new WalkIndex(\n            openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n            this,\n          )\n        : undefined\n    return {\n      segments,\n      links,\n      walks,\n      refNames: new PanSNRefNames(walks?.file ?? segments, this),\n    }\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.fine.walks?.haplotypeNames(opts)\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  // getFeatures reads a walk file from the chunk before the window\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    const { walks, refNames } = this.fine\n    return refNames.regionBytes(\n      regions,\n      opts,\n      walks &&\n        ((refName, { start, end }) =>\n          walks.reader.queryStart(start, { ...opts, refName, end })),\n    )\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolveMapped(query, opts)\n      if (tabixRefName !== undefined) {\n        const { walks } = this.fine\n        const emit = (feature: Feature) => {\n          observer.next(feature)\n        }\n        await (walks\n          ? this.walkFeatures(walks, tabixRefName, query, opts, emit)\n          : this.segmentFeatures(tabixRefName, query, opts, emit))\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n\n  // A walk-indexed graph's reference nodes are its ref rows' steps\n  private async walkFeatures(\n    walks: WalkIndex,\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    const nodes = await updateStatus(\n      'Downloading walks',\n      opts.statusCallback,\n      () => walks.referenceNodes(tabixRefName, query, opts),\n    )\n    for (const node of nodes) {\n      const id = String(node.id)\n      emit(\n        new SimpleFeature({\n          uniqueId: id,\n          refName: query.refName,\n          start: node.start,\n          end: node.end,\n          name: id,\n          type: 'segment',\n          rank: 0,\n          stableName: node.refName,\n        }),\n      )\n    }\n  }\n\n  private async segmentFeatures(\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    await updateStatus('Downloading segments', opts.statusCallback, () =>\n      getLines(this.fine.segments, tabixRefName, query.start, query.end, {\n        signal: opts.signal,\n        lineCallback: line => {\n          const { segment, anchored } = parseSegmentRow(line)\n          // An anchored index also returns the alleles under the region,\n          // which lie on other stable sequences and have no place on this one\n          if (anchored && segment.refName !== tabixRefName) {\n            return\n          }\n          // `samples` lists the haplotypes whose paths visit the segment and\n          // `sampleCount` counts them. A lane's color reads the count, and\n          // a count in jexl would otherwise rely on `.length` resolving\n          // through a member access on an array.\n          const samples = segmentSamples(segment)\n          emit(\n            new SimpleFeature({\n              uniqueId: segment.id,\n              refName: query.refName,\n              start: segment.start,\n              end: segment.end,\n              name: segment.id,\n              type: 'segment',\n              rank: segment.rank,\n              stableName: segment.refName,\n              ...(samples && { samples, sampleCount: samples.length }),\n            }),\n          )\n        },\n      }),\n    )\n  }\n\n  // The graph around a region for GraphGenomeView: GFA text (rgfaCut), or a\n  // walk-indexed graph's tables (WalkIndex.subgraph). `tier: 'coarse'` reads\n  // the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops, signal, tier } = opts\n    const index = this.index(tier)\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n    if (tabixRefName === undefined) {\n      throw new Error(unmappedRegionMessage(region))\n    }\n    if (index.walks) {\n      return index.walks.subgraph(tabixRefName, region, opts)\n    }\n    return rgfaCut(\n      index,\n      { refName: tabixRefName, start: region.start, end: region.end },\n      { hops, signal },\n    )\n  }\n}\n"],
-  "mappings": "ufA6BA,IAAqBA,EAArB,cAA8CC,CAA+C,CAA7F,kCAGE,KAAiB,KAAO,KAAK,UAAU,CAAC,CAAC,EAFzC,YAAc,aAAe,CAAC,cAAe,aAAa,EASlD,UAAUC,EAA6B,CAC7C,IAAMC,EAAWC,EACf,KACA,CAAC,GAAGF,EAAO,kBAAkB,EAC7B,CAAC,GAAGA,EAAO,eAAe,CAC5B,EACMG,EAAQD,EACZ,KACA,CAAC,GAAGF,EAAO,eAAe,EAC1B,CAAC,GAAGA,EAAO,YAAY,CACzB,EACMI,EAA8B,KAAK,QAAQ,eAAe,EAC1DC,EACJL,EAAM,SAAW,GAAKM,EAAcF,CAAa,EAC7C,IAAIG,EACFL,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,IACF,EACA,OACN,MAAO,CACL,SAAAD,EACA,MAAAE,EACA,MAAAE,EACA,SAAU,IAAIG,EAAcH,GAAO,MAAQJ,EAAU,IAAI,CAC3D,CACF,CAMA,MAAM,kBAAkBQ,EAAoB,CAAC,EAAG,CAC9C,OAAO,KAAK,KAAK,OAAO,eAAeA,CAAI,CAC7C,CAEQ,MAAMC,EAAqB,OAAQ,CACzC,OAAIA,IAAS,OACJ,KAAK,MAEd,KAAK,SAAW,KAAK,UAAU,CAAC,QAAQ,CAAC,EAClC,KAAK,OACd,CAEA,MAAM,YAAYD,EAAoB,CAAC,EAAG,CACxC,OAAO,KAAK,KAAK,SAAS,iBAAiBA,CAAI,CACjD,CAGA,MAAM,kBAAkBE,EAAmBF,EAAoB,CAAC,EAAG,CACjE,GAAM,CAAE,MAAAJ,EAAO,SAAAO,CAAS,EAAI,KAAK,KACjC,OAAOA,EAAS,YACdD,EACAF,EACAJ,IACG,CAACQ,EAAS,CAAE,MAAAC,EAAO,IAAAC,CAAI,IACtBV,EAAM,OAAO,WAAWS,EAAO,CAAE,GAAGL,EAAM,QAAAI,EAAS,IAAAE,CAAI,CAAC,EAC9D,CACF,CAEA,MAAa,mBAAoB,CAC/B,MAAO,EACT,CAEA,YAAYC,EAAeP,EAAoB,CAAC,EAAG,CACjD,OAAOQ,EAA0B,MAAMC,GAAY,CACjD,IAAMC,EAAe,MAAM,KAAK,KAAK,SAAS,cAAcH,EAAOP,CAAI,EACvE,GAAIU,IAAiB,OAAW,CAC9B,GAAM,CAAE,MAAAd,CAAM,EAAI,KAAK,KACjBe,EAAQC,GAAqB,CACjCH,EAAS,KAAKG,CAAO,CACvB,EACA,MAAOhB,EACH,KAAK,aAAaA,EAAOc,EAAcH,EAAOP,EAAMW,CAAI,EACxD,KAAK,gBAAgBD,EAAcH,EAAOP,EAAMW,CAAI,EAC1D,CACAF,EAAS,SAAS,CACpB,EAAGT,EAAK,MAAM,CAChB,CAGA,MAAc,aACZJ,EACAc,EACAH,EACAP,EACAW,EACA,CACA,IAAME,EAAQ,MAAMC,EAClB,oBACAd,EAAK,eACL,IAAMJ,EAAM,eAAec,EAAcH,EAAOP,CAAI,CACtD,EACA,QAAWe,KAAQF,EAAO,CACxB,IAAMG,EAAK,OAAOD,EAAK,EAAE,EACzBJ,EACE,IAAIM,EAAc,CAChB,SAAUD,EACV,QAAST,EAAM,QACf,MAAOQ,EAAK,MACZ,IAAKA,EAAK,IACV,KAAMC,EACN,KAAM,UACN,KAAM,EACN,WAAYD,EAAK,OACnB,CAAC,CACH,CACF,CACF,CAEA,MAAc,gBACZL,EACAH,EACAP,EACAW,EACA,CACA,MAAMG,EAAa,uBAAwBd,EAAK,eAAgB,IAC9DkB,EAAS,KAAK,KAAK,SAAUR,EAAcH,EAAM,MAAOA,EAAM,IAAK,CACjE,OAAQP,EAAK,OACb,aAAcmB,GAAQ,CACpB,GAAM,CAAE,QAAAC,EAAS,SAAAC,CAAS,EAAIC,EAAgBH,CAAI,EAGlD,GAAIE,GAAYD,EAAQ,UAAYV,EAClC,OAMF,IAAMa,EAAUC,EAAeJ,CAAO,EACtCT,EACE,IAAIM,EAAc,CAChB,SAAUG,EAAQ,GAClB,QAASb,EAAM,QACf,MAAOa,EAAQ,MACf,IAAKA,EAAQ,IACb,KAAMA,EAAQ,GACd,KAAM,UACN,KAAMA,EAAQ,KACd,WAAYA,EAAQ,QACpB,GAAIG,GAAW,CAAE,QAAAA,EAAS,YAAaA,EAAQ,MAAO,CACxD,CAAC,CACH,CACF,CACF,CAAC,CACH,CACF,CAKA,MAAM,YACJE,EACAzB,EAA+B,CAAC,EACL,CAC3B,GAAM,CAAE,KAAA0B,EAAM,OAAAC,EAAQ,KAAA1B,CAAK,EAAID,EACzB4B,EAAQ,KAAK,MAAM3B,CAAI,EACvBS,EAAe,MAAMkB,EAAM,SAAS,QAAQH,EAAQ,CAAE,OAAAE,CAAO,CAAC,EACpE,GAAIjB,IAAiB,OACnB,MAAM,IAAI,MAAMmB,EAAsBJ,CAAM,CAAC,EAE/C,OAAIG,EAAM,MACDA,EAAM,MAAM,SAASlB,EAAce,EAAQzB,CAAI,EAEjD8B,EACLF,EACA,CAAE,QAASlB,EAAc,MAAOe,EAAO,MAAO,IAAKA,EAAO,GAAI,EAC9D,CAAE,KAAAC,EAAM,OAAAC,CAAO,CACjB,CACF,CACF",
-  "names": ["RgfaTabixAdapter", "BaseFeatureDataAdapter", "under", "segments", "openTabixSlot", "links", "walksLocation", "walks", "locationIsSet", "WalkIndex", "PanSNRefNames", "opts", "tier", "regions", "refNames", "refName", "start", "end", "query", "ObservableCreate", "observer", "tabixRefName", "emit", "feature", "nodes", "updateStatus", "node", "id", "SimpleFeature", "getLines", "line", "segment", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "signal", "index", "unmappedRegionMessage", "rgfaCut"]
-}

package/dist/chunks/WalkTabixSyntenyAdapter-3WRVNDLB.js

@@ -1,2 +0,0 @@
-import{a as K}from"./chunk-OJWBLPPH.js";import{b as q,d as U,e as X,f as O,g as z,h as G}from"./chunk-HF4H6LQI.js";import"./chunk-QV7SSOMJ.js";import{a as H}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import{C as j,E as D,i as $}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{a as A,c as I,d as W,g as F,h as w,i as x}from"./chunk-6SWXMRAV.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as R}from"./chunk-TENPGIPX.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 v(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function P(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=P(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=v(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function E(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=>P(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=v(a),n=v(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 d=e(s),h=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);E(m,"I",h[te]-h[ee+1]),E(m,"D",d[g]-d[p[k-1][1]+1])}E(m,"=",i(s[g]))});let[b,S]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:h[b],queryEnd:h[S+1],targetStart:d[p[0][1]],targetEnd:d[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+=P(r,l):f!==void 0&&(o+=P(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 q{constructor(){super(...arguments);this.walks=new K(j(this,["walksLocation"],["walksIndex"]),this);this.refNames=new D(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&&A(o)!==s).map(o=>({name:O(n,o),label:o,group:A(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.resolve(e,{signal:t.signal});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=$(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 ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),d=c.filter(m=>m.name===e),h=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&h(m)>=0).sort((m,b)=>h(m)-h(b)).flatMap(m=>d.flatMap(b=>p(m,b).map(S=>C({chain:S,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(d=>f(N).flatMap(h=>u(h,d).map(y=>C({chain:y,target:d,query:h,assemblyName:c.queryAssemblyName,refName:W(d.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return H(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=U(t),o=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let l of o)a.next(l)}a.complete()},t.signal)}};export{L as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-3WRVNDLB.js.map

package/dist/chunks/chunk-6VNU7SD4.js

@@ -1,2 +0,0 @@
-import{h as B,k as M,n as F}from"./chunk-7RJMG6I2.js";import{b as O,h as _}from"./chunk-2KVE7YAS.js";import{J as b,P as A}from"./chunk-S333HOG5.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),i(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(r,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(r,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(W,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:M(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(r,{children:"Where genes on the backbone come from"})}),t(W,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(r,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),i(y,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:d.section,children:t(r,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(p,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(r,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(p,{label:"Layout quality",value:String(e.layoutQuality),options:S.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(r,{children:"The engine's iteration budget; higher is slower"})}),t(p,{label:"Bubble spread",value:e.bubbleSpread,options:_,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(r,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(r,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),he=$;export{f as a,he as b};
-//# sourceMappingURL=chunk-6VNU7SD4.js.map

package/dist/chunks/chunk-GRTN25B6.js

@@ -1,3 +0,0 @@
-import{b as jn,g as _o,h as $o,j as ct,k as dt,l as Ho,m as Wo}from"./chunk-7RJMG6I2.js";import{$ as ot,$b as it,A as Xn,Aa as no,B as Je,Ba as oo,C as Vn,D as qe,Da as ro,Db as ko,E as Ct,Ea as so,Eb as xo,Fb as Dt,Gb as Ro,Ha as ce,Hb as So,I as Bt,J as Ze,Ja as io,Jb as vo,L as Ot,M as Pe,Mb as ee,N as Qe,O as K,Ob as Mo,P as et,Pb as Lo,Qb as No,R as tt,Ra as co,Rb as Po,S as nt,Sb as Ao,Tb as To,U as _t,Ub as Go,Vb as Eo,W as B,Wa as po,Xb as Io,Yb as Co,Z as Ae,Zb as Bo,_ as Te,_b as Oo,aa as Yn,b as Ln,bb as lo,bc as Fo,cc as Do,d as Pt,db as mo,ea as Jn,eb as uo,fa as rt,fb as ho,ga as qn,gb as fo,h as Gt,i as Gn,ia as Zn,j as Et,ja as Qn,k as En,l as In,lb as go,m as Me,n as ue,ob as Ft,q as Le,qb as wo,r as Q,ra as eo,rb as bo,s as ie,sb as yo,ta as to,ua as Wt,x as Dn,xa as Ge}from"./chunk-WLRRI35A.js";import{A as zn,B as Un,C as Kn,D as Ht,a as Z,b as It,c as Cn,d as Bn,e as On,g as _n,i as $n,p as Ue,s as Hn,t as Ne,u as Wn,v as Fn,w as Ke,z as $t}from"./chunk-VZQ6VOUP.js";import{A as Se,B as An,D as Tn,K as je,N as ve,O as Ye,T as ze,a as j,b as ye,i as ke,n as xe,o as se,p as At,r as Nn,s as Pn,v as Tt,z as Re}from"./chunk-S333HOG5.js";import{b as at,c as st,e as ao}from"./chunk-P3FBI5ML.js";import{b as St,c as vt,d as Mt,f as Lt}from"./chunk-6WUWQX2P.js";import{e as Rn,l as Mn,m as Nt}from"./chunk-G53BI7VK.js";import{a as bn,b as yn,d as kn,f as le,g as I,h as we,i as q,j as kt,k as ae,l as xt,m as Rt,n as be,r as H,w as vn}from"./chunk-LE7FZM6Y.js";import{d as V}from"./chunk-JRJHXLGP.js";import{a as me,c as xn,d as Ve}from"./chunk-6SWXMRAV.js";import{d as Sn}from"./chunk-IKJZPPOA.js";import{f as gn,g as yt,h as wn,j as U}from"./chunk-TENPGIPX.js";import{b as D}from"./chunk-JMBDTNUR.js";var de=JBrowseExports["@mui/material/SvgIcon"],Kr=e=>de!=null&&e in Object(de)?de[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@mui/material/SvgIcon' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),W=Kr("createSvgIcon"),ds=de&&de.__esModule?de.default:de;function Xo(e){if(typeof e!="object"||e===null)return!1;let t=e;return typeof t.horizontalScroll=="function"&&typeof t.zoomTo=="function"&&"coarseDynamicBlocks"in t&&"dynamicBlocks"in t}function Vo(e){return e.reduce((t,n)=>t&&t.end-t.start>=n.end-n.start?t:n,void 0)}function jo(e,t){let n=Vo(e.dynamicBlocks.contentBlocks.filter(r=>r.refName===t.refName&&r.assemblyName===t.assemblyName)),{bpPerPx:o}=e;if(!n||!(o>0))return;let a=n.offsetPx-e.offsetPx;return n.reversed?{scale:-1/o,translateX:a+n.end/o}:{scale:1/o,translateX:a-n.start/o}}function us(e){let t=Vo(e.dynamicBlocks.contentBlocks),n=t?.displayedRegionIndex===void 0?void 0:e.displayedRegions[t.displayedRegionIndex];return t&&e.bpPerPx>0?{refName:t.refName,assemblyName:t.assemblyName,start:t.start,end:t.end,bpPerPx:e.bpPerPx,span:e.bpPerPx*e.width,regionStart:n?.start??t.start,regionEnd:n?.end??t.end}:void 0}function Jr(e,t,n=!0){let o=e.end-e.start,a=n?Math.max(0,Math.min(e.span,(t-o)/2)):0,r=Math.max(e.regionStart,Math.floor(e.start-a)),s=Math.min(e.regionEnd,Math.ceil(e.end+a)),i=s-r-t;return i>0&&(r+=Math.floor(i/2),s-=Math.ceil(i/2)),{refName:e.refName,assemblyName:e.assemblyName,start:r,end:s}}function hs(e,t,n=!0){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;if(n)return e.start<=t.start+1&&t.end<=e.end+1;let o=Jr(t,1/0,!1);return Math.abs(e.start-o.start)<1&&Math.abs(e.end-o.end)<1}var qr=/^[^#]+#\d+$/;function Zr(e,t){let n=e.assemblyNameToPanSN??{},o=new Set(Object.values(n)),a={};for(let{name:r,aliases:s}of t){let i=s.find(c=>qr.test(c));i!==void 0&&!o.has(i)&&(a[r]=i)}return Object.keys(a).length===0?e:{...e,assemblyNameToPanSN:{...a,...n}}}function Qr(e,t){let n=s=>t.find(i=>i.name===s||i.aliases.includes(s))?.name??s,o=e.assemblyNames??[],a=e.assemblyNameToPanSN??{};if([...o,...Object.keys(a)].every(s=>n(s)===s))return e;let r=new Map;for(let[s,i]of Object.entries(a)){let c=n(s);(c===s||!r.has(c))&&r.set(c,i)}for(let s of o){let i=n(s);i!==s&&!r.has(i)&&r.set(i,s)}return{...e,assemblyNames:o.map(n),assemblyNameToPanSN:Object.fromEntries(r)}}var ea=new Set(["GbzBaseSyntenyAdapter","WalkTabixSyntenyAdapter"]);function Yo(e,t){let n=V(t,"adapter");if(!ea.has(n.type)&&!jn(n))return n;let o=U(e).assemblyManager.assemblyList.map(a=>({name:V(a,"name"),aliases:V(a,"aliases")??[]}));return Zr(Qr(n,o),o)}var ta=1,na=.015;function pt({graph:e,span:t,rowY:n,positions:o}){let a=t*na,r=In(e),s=new Map(e.nodes.map(m=>[m.id,m])),i=[];for(let m of r){let p=m.refSpan-m.pathLength;p>=ta&&i.push({nodeIds:m.nodeIds,bp:p});let l=Math.max(m.refSpan,a),u=m.pathLength>0?l/m.pathLength:0;m.nodeIds.forEach((h,f)=>{let g=s.get(h);if(g){let w=m.nodeOffsets[f],x=l/m.nodeIds.length,v=k=>m.start+k*u,y=n(g);o[h]=u?[{x:v(w),y},{x:v(w+g.length),y}]:[{x:m.start+f*x,y},{x:m.start+(f+1)*x,y}]}})}let c=Z(e),d=Object.keys(o);for(let m of d){let p=o[m].at(-1).x;for(let l of c.get(m)??[]){let u=s.get(l);if(u&&!(l in o)){let h=n(u);o[l]=[{x:p,y:h},{x:p+a,y:h}],d.push(l)}}}return i}function oa(e,t){let n=new Map;for(let a of e.nodes)if(we(a)){let r=me(a.stable.refName);n.set(r,(n.get(r)??0)+a.length)}let o=new Map(t.map((a,r)=>[a,r]));return[...n.keys()].sort((a,r)=>(o.get(a)??1/0)-(o.get(r)??1/0)||n.get(r)-n.get(a)||a.localeCompare(r))}function zo(e,t,n=[]){let o=q(e),a=oa(e,n);if(o.length===0||a.length===0)return;let r=be(o,t),s=new Map(a.map((l,u)=>[l,u+1])),i=ae(o),c=a.length+1,d=pt({graph:e,span:r,rowY:l=>{let u=l.stable;return((u?s.get(me(u.refName)):void 0)??c)*j},positions:i}),p=[{label:me(o[0].stable.refName),y:0},...a.map(l=>({label:l,y:s.get(l)*j}))];return{nodePositions:i,rowLabels:p,sampleRows:a,referenceAxis:!0,pixelRows:!0,alleleDeletions:d}}function ra(e){let t=new Set;for(let n of e.nodes)n.stable&&t.add(n.stable.rank);return new Map([...t].sort((n,o)=>n-o).map((n,o)=>[n,o]))}function Uo(e,t){let n=q(e);if(n.length===0)return;let o=be(n,t),a=ra(e),r=ae(n),s=pt({graph:e,span:o,rowY:c=>(c.stable?a.get(c.stable.rank)??a.size:a.size)*j,positions:r}),i=[...a].map(([c,d])=>({label:c===0?"Reference (rank 0)":`Rank ${c}`,y:d*j}));return{nodePositions:r,rowLabels:i,referenceAxis:!0,pixelRows:!0,alleleDeletions:s}}var aa=12,Xt=j;function Ko(e){return 10+8*Math.log2(1+e.length)}function te(e,t){return e<t?-1:e>t?1:0}function qo(e,t){return te(e.at,t.at)||te(e.side,t.side)||te(e.hops,t.hops)}var Jo={at:1/0,side:0,hops:0};function Vt(e){let t=new Map(e.nodes.map(o=>[o.id,o])),n=ca(e);return e.nodes.map(o=>o.id).sort((o,a)=>qo(n.get(o)??Jo,n.get(a)??Jo)||te(t.get(o).name,t.get(a).name)||te(o,a))}function sa(e,t){let n=new Set(e.nodes.map(m=>m.id)),o=new Map(t.map(m=>[m.id,m.stable.start])),a=new Map,r=new Map;t.forEach((m,p)=>{r.set(m.id,t[p-1]?.id),a.set(m.id,t[p+1]?.id)});let s=t[0]?.id,i=(m,p)=>{let l=a.get(m);a.set(m,p),r.set(p,m),a.set(p,l),l!==void 0&&r.set(l,p)},c=(m,p)=>{let l=r.get(m);l===void 0?(s=p,r.set(p,void 0),a.set(p,m),r.set(m,p)):i(l,p)};for(let m of e.paths??[]){let p=0,l=0,u;for(let w of m.nodeIds){let x=o.get(w);x!==void 0&&(u!==void 0&&x!==u&&(x>u?p++:l++),u=x)}let h=l>p?[...m.nodeIds].reverse():m.nodeIds,f,g=new Set;for(let w of h)if(a.has(w)){if(f===void 0)for(let x of g)c(w,x);f=w}else n.has(w)&&(f===void 0?g.add(w):(i(f,w),f=w))}let d=[];for(let m=s;m!==void 0;m=a.get(m))d.push(m);return d}function ia(e,t,n){let o=[...t.entries()].sort(([i,c],[d,m])=>qo(c,m)||te(i,d)).map(([i])=>i),a=o.length;for(let i of o){let c=t.get(i);for(let d of e.get(i)??[])n.has(d)&&!t.has(d)&&(t.set(d,{at:c.at,side:1,hops:c.hops+1}),o.push(d))}let r=new Set(o.slice(a)),s=new Set;for(let i of r){if(s.has(i))continue;let{at:c}=t.get(i),d=[i];s.add(i);let m=!0;for(let p of d){let{hops:l}=t.get(p),u=!0,h=!1;for(let f of e.get(p)??[]){let g=t.get(f);g&&(g.at===c&&r.has(f)?(u&&=g.hops<=l,s.has(f)||(s.add(f),d.push(f))):g.at!==c&&(h||=g.at<c,m&&=g.at<c))}m&&=!u||h}if(m)for(let p of d){let l=t.get(p);t.set(p,{...l,side:-1,hops:-l.hops})}}}function ca(e){let t=e.nodes.filter(I).sort((o,a)=>te(o.stable.start,a.stable.start)||te(o.name,a.name)),n=new Map;return sa(e,t).forEach((o,a)=>{n.set(o,{at:a,side:0,hops:0})}),ia(Z(e),n,new Set(e.nodes.map(o=>o.id))),n}function da(e){let t=new Map(e.nodes.map(p=>[p.id,p])),n=Vt(e),o=new Map(n.map((p,l)=>[p,l])),a=p=>I(t.get(p)),r=new Map(n.map(p=>[p,[]])),s=new Map(n.map(p=>[p,[]])),i=(p,l)=>{r.get(l).push(p),s.get(p).push(l)};for(let p of e.edges)p.from===p.to||!o.has(p.from)||!o.has(p.to)||(o.get(p.from)<o.get(p.to)?i(p.from,p.to):i(p.to,p.from));let c=n.filter(a);for(let p=1;p<c.length;p++)i(c[p-1],c[p]);let d=new Map;for(let p of n){let l=0;for(let u of r.get(p))l=Math.max(l,d.get(u)+1);d.set(p,l)}for(let p=n.length-1;p>=0;p--){let l=n[p],u=s.get(l);if(a(l)||u.length===0)continue;let h=1/0;for(let w of u)h=Math.min(h,d.get(w));let f=d.get(l),g=Math.max(f,h-1);d.set(l,Math.floor((f+g)/2))}let m=[];for(let p of n)(m[d.get(p)]??=[]).push(p);return{layers:m,layerOf:d,preds:r}}function Zo(e){if(!e.nodes.some(I))return;let t=new Map(e.nodes.map(p=>[p.id,p])),n=p=>I(t.get(p)),{layers:o,layerOf:a,preds:r}=da(e),s=o.map(p=>{let l=0;for(let u of p)l=Math.max(l,Ko(t.get(u)));return l}),i=[],c=0;for(let p=0;p<o.length;p++)i[p]=c,c+=s[p]+aa;let d=new Map;for(let p of o){let l=[];for(let h of p){if(n(h)){d.set(h,0);continue}let f=r.get(h).filter(w=>d.has(w)),g=0;for(let w of f)g+=d.get(w)/f.length;l.push({id:h,ideal:g===0?Xt:g})}l.sort((h,f)=>h.ideal-f.ideal);let u=new Set([0]);for(let{id:h,ideal:f}of l){let g=Math.round(f/Xt);g===0&&(g=f>=0?1:-1);for(let w=1;u.has(g);w++)u.has(g+w)?u.has(g-w)||(g-=w):g+=w;u.add(g),d.set(h,g*Xt)}}let m={};for(let p of e.nodes){let l=a.get(p.id),u=Ko(p),h=i[l]+s[l]/2,f=d.get(p.id);m[p.id]=[{x:h-u/2,y:f},{x:h+u/2,y:f}]}return{nodePositions:m,referenceAxis:!1,pixelRows:!0}}var lt=1.3;function mt(e){return Math.max(e.reference.bp,...e.rows.map(t=>t.bp))}function he(e,t={rowPx:j,readouts:!0}){return{maxX:e.origin+mt(e)*(t.readouts?lt:1),maxY:e.rows.length*t.rowPx}}function fe(e,t,n){return e?n&&!n.labelled?[]:[e.reference,...e.rows].map((o,a)=>({label:o.label,y:a*(n?.rowPx??j)})):t?.rowLabels??[]}function jt(e,t){let n=ue(e,t);return n&&Qo(e,n,t)}function Qo(e,t,n){let o=q(e);if(o.length===0)return;let a=n?o.filter(s=>kt(s,n)):o;return{nodePositions:ae(a.length>0?a:o),rowLabels:fe(t),referenceAxis:!0,pixelRows:!0,extent:he(t)}}var nr="Force-directed layout",ge=e=>e.nodes.some(I),er=e=>ge(e)&&(e.paths?.length??0)>1,tr=e=>ge(e)&&e.nodes.some(we),ut=[{value:"auto",label:"Anchored",description:"x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.",run:Uo,cutMargins:!0,wholeWalks:!1,available:ge,drawsLocally:ge,drawsNodes:!0},{value:"samplerows",label:"Sample rows",description:"x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.",run:zo,cutMargins:!0,wholeWalks:!1,available:tr,drawsLocally:tr,drawsNodes:!0},{value:"walkrows",label:"Walk rows",description:"x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs a reference and two or more walks.",run:jt,cutMargins:!1,wholeWalks:!0,available:er,drawsLocally:er,drawsNodes:!1},{value:"ordered",label:"Ordered",description:"x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.",run:Zo,cutMargins:!1,wholeWalks:!1,available:ge,drawsLocally:ge,drawsNodes:!0},{value:"tubemap",label:"Tube map",description:"sequenceTubeMap: every path a coloured tube through boxed nodes, columns in node order and node widths log-scaled. Needs P or W lines.",run:Gn,cutMargins:!1,wholeWalks:!1,available:Gt,drawsLocally:Gt,drawsNodes:!1},{value:"tubemapref",label:"Tube map on reference",description:"The tube map with each column at the reference bp it covers, so the tubes line up with the tracks around them. Needs P or W lines and a reference path.",run:En,cutMargins:!0,wholeWalks:!1,available:Et,drawsLocally:Et,drawsNodes:!1},{value:"force",label:nr,description:"OGDF FMMM (wasm) or stress, whichever engine is chosen.",run:()=>{},cutMargins:!1,wholeWalks:!1,available:()=>!0,drawsLocally:()=>!1,drawsNodes:!0}],pa=ut.map(e=>e.value);function Yt(e,t){return!Y(e).drawsLocally(t)}function Y(e){return ut.find(t=>t.value===e)??ut[0]}function zt(e){return e.walkStrip&&e.mode.drawsNodes&&!e.drawsPicture&&!e.popped&&!e.host&&e.walks>1}function Ut(e,t){return e.wholeWalks||t.walkStrip&&!t.host}var Ee=6,ar=260,la=11,ma=3,ua="#111",or=3;function Kt(e,t,n){let o=e.pathVisits?.get(n.name)??[],a=[];for(let r of t){let s=r.axis;if(!s)continue;let i=H(r.name).name;for(let c of o){if(c.path!==i)continue;let{start:d,end:m}=Xn(s,c.start,c.start+n.length);m>0&&d<r.bp&&a.push({row:r.name,start:d,bp:m-d})}}return a}var rr=new WeakMap;function ha(e,t){let n=rr.get(e);if(n||(n=new Map,rr.set(e,n)),n.has(t))return n.get(t);let o=new Map(e.nodes.map(i=>[i.id,i.length])),a=H(t).name,r=(e.paths??[]).filter(i=>H(i.name).name===a),s;if(r.every(i=>i.start!==void 0)){s={ids:[],starts:[],ends:[]};for(let i of[...r].sort((c,d)=>c.start-d.start)){let c=i.start;for(let d of i.nodeIds){let m=o.get(d)??0;s.ids.push(d),s.starts.push(c),s.ends.push(c+m),c+=m}}}return n.set(t,s),s}function fa(e,t,n,o){let a=t.axis,r=a&&ha(e,t.name);if(!a||!r||n<0||n>t.bp)return;let s=a.reversed?a.start-n:a.start+n,i=.5/o,c=Je(a,t.bp),d=Math.max(s-i,c.start),m=Math.min(s+i,c.end),p=kn(r.starts.length,f=>r.ends[f]<=d),l,u=-1,h=!1;for(let f=p;f<r.starts.length&&r.starts[f]<m;f++){let g=r.ends[f]-r.starts[f],w=r.starts[f]<=s&&s<r.ends[f];(g>u||g===u&&w&&!h)&&(u=g,l=r.ids[f],h=w)}return l}function Ie(e,t){let n=t.maxHeight??ar,o=t.labelPx??Math.max(...[e.reference,...e.rows].map(u=>u.label.length))*se+16,a=e.rows.length+1,{rowPx:r,barPx:s,labelled:i,readouts:c}=Ze(a,n-2*Ee,ma),d=Math.max(mt(e),1),m=i?o:Ee,l=Math.max(1,t.width-m-Ee)/(d*(c?lt:1));return{scaleX:l,scaleY:1,translateX:m-e.origin*l,translateY:Ee+r/2,width:t.width,height:a*r+2*Ee,rowPx:r,barPx:s,readouts:c,labelled:i,boxesGenes:qe(r,s)}}function ga(e,t,n,o){let a=Math.round((o-t.translateY)/t.rowPx),r=[e.reference,...e.rows][a],s=(n-t.translateX)/t.scaleX-e.origin;return r&&a>=0&&s>=0&&s<=r.bp?{index:a,row:r,offset:s}:void 0}function wa(e,t,n){let o=new Map([e.reference,...e.rows].map((r,s)=>[r.name,s])),a=r=>(e.origin+r)*t.scaleX+t.translateX;return Le("g",{"data-testid":"graph-walk-marks"},...n.flatMap(r=>{let s=o.get(r.row);if(s===void 0)return[];let i=s*t.rowPx+t.translateY,c=a(r.start),d=Math.max(2,r.bp*t.scaleX),m=p=>Le("rect",{x:c,y:p,width:d,height:or,fill:ua});return[m(i-t.barPx/2-or-1),m(i+t.barPx/2+1)]}))}function Jt(e,t,n=new Set){return Le("g",{"font-family":"sans-serif","font-size":la,fill:"#333"},...(t.labelled?[e.reference,...e.rows]:[]).map((o,a)=>Le("text",{x:6,y:a*t.rowPx+t.translateY+4,"font-weight":n.has(o.name)?600:void 0},o.label)))}function qt(e,t,n){if(t?.size)return e.boxesGenes?n:{untracked:0,unread:0,...n,crowded:!0}}function ne(e){return`${e.refName}:${(e.start+1).toLocaleString()}-${e.end.toLocaleString()}`}function ba(e,t,n=o=>o){return t?{deletion:{bp:`${t.bp.toLocaleString()} bp`,where:ne(t)}}:{ends:`${n(e.from)}${e.fromStrand??""} \u2192 ${n(e.to)}${e.toStrand??""}`}}function sr(e){return le(e)?ir(e):void 0}function ir(e){return{sample:me(e.stable.refName),haplotype:xn(e.stable.refName),refName:Ve(e.stable.refName),start:e.stable.start,end:e.stable.start+e.length}}function ya(e,t){let n=[...e].sort((r,s)=>r.start-s.start),o,a;for(let r of n)a=a&&r.start-a.end<=t?{start:a.start,end:Math.max(a.end,r.end)}:{start:r.start,end:r.end},(!o||a.end-a.start>o.end-o.start)&&(o=a);return o}function ka(e){return`${e.haplotype??e.sample}\0${e.refName}`}function cr(e,{maxGap:t=1/0}={}){let n=new Map;for(let a of e.nodes)if(le(a)){let r=ir(a),s=ka(r),i=n.get(s);i?(i.spans.push({start:r.start,end:r.end}),i.rank=Math.min(i.rank,a.stable.rank)):n.set(s,{sample:r.sample,haplotype:r.haplotype,refName:r.refName,rank:a.stable.rank,spans:[{start:r.start,end:r.end}]})}let o=new Map;for(let a of n.values()){let r=ya(a.spans,t);if(r){let s={sample:a.sample,haplotype:a.haplotype,refName:a.refName,start:r.start,end:r.end,rank:a.rank,nodeCount:a.spans.length},i=a.haplotype??a.sample,c=o.get(i);(!c||s.nodeCount>c.nodeCount)&&o.set(i,s)}}return[...o.values()].sort((a,r)=>+(a.rank!==0)-+(r.rank!==0)||a.sample.localeCompare(r.sample)||(a.haplotype??"").localeCompare(r.haplotype??""))}function Ce(e,t){return(t.haplotype===void 0?void 0:e(t.haplotype))??e(t.sample)}function dr(e,t){return e.flatMap(n=>{let o=Ce(t,n);return o===void 0?[]:[{...n,sample:o}]})}function ht(e){return`${e.refName}:${e.start+1}-${e.end}`}function z(e){return typeof e=="object"&&e!==null}function xa(e){return z(e)&&e.type==="LinearGenomeView"&&typeof e.id=="string"&&typeof e.navToLocString=="function"&&Array.isArray(e.assemblyNames)}function Ra(e){return e.flatMap(t=>z(t)&&Array.isArray(t.views)?[t,...t.views]:[t])}function Be({views:e,connectedViewId:t,assemblyName:n}){let o=Ra(e).filter(r=>xa(r)).filter(r=>r.assemblyNames.includes(n));return o.find(r=>r.id===t)??(o.length===1?o[0]:void 0)}function Zt(e,t){let n=e.assemblyManager;return n?.has(t)?n.get(t)?.name??t:t}function Lc(e,t){let n=e.assemblyManager,o=n?.has(t.assemblyName)?n.get(t.assemblyName):void 0;return o?{...t,assemblyName:o.name,refName:o.getCanonicalRefName2?.(t.refName)??t.refName}:t}function Qt(e,t){let n=V(t,"assemblyNames");return Array.isArray(n)?n.filter(o=>typeof o=="string").map(o=>Zt(e,o)):[]}function lr(e,t,n){n.catch(o=>{console.error(`[GraphGenomeView] ${t}`,o),e.notifyError?.(`${t}: ${o}`,o)})}var Sa=1e3;function en(e,t=Sa){let n=Math.max(0,Math.ceil((t-(e.end-e.start))/2));return{...e,start:Math.max(0,e.start-n),end:e.end+n}}function mr(e,t){return t?e.map(n=>n.rank===0?{...n,sample:t.assemblyName,haplotype:void 0,refName:t.refName,start:t.start,end:t.end}:n):e}function Nc({session:e,location:t,assembly:n,connectedViewId:o,tracks:a=[]}){let r=Be({views:e.views,connectedViewId:o,assemblyName:n}),s;return r?(lr(e,`Could not show ${n} ${ne(t)}`,Promise.resolve(r.navToLocString(ht(t),n))),s=r.id):s=e.addView("LinearGenomeView",{displayName:`${n} \u2014 ${ne(t)}`,init:{assembly:n,loc:ht(t),tracks:a}}).id,s}function Pc({session:e,location:t,assembly:n,connectedViewId:o}){Be({views:e.views,connectedViewId:o,assemblyName:n})&&e.addHighlight?.({refName:t.refName,start:t.start,end:t.end,assemblyName:n})}function pr(e,t){let n=t===void 0?void 0:e.tracks.find(o=>V(o,"trackId")===t);return n?Qt(e,n):[]}function Ac({session:e,contributors:t,trackId:n,graphTrackId:o}){let a=pr(e,o),r=pr(e,n),s=t.filter(d=>r.includes(d.sample)),i=s.length>=2?s:t,c={init:{views:i.map(d=>({assembly:d.sample,loc:ht(d),...o!==void 0&&a.includes(d.sample)?{tracks:[o]}:{}})),tracks:n?i.slice(1).map(()=>[n]):[],collapseEmptyRows:!0}};lr(e,"Could not open the synteny view",e.launchView("LinearSyntenyView",c))}function Oe(e,t,n){let o=new Map;for(let r of e.nodes)if(le(r)){let{refName:s}=r.stable;if(n[r.id]?.length){let i=o.get(s)??o.set(s,{nodes:[],reach:0}).get(s);i.nodes.push(r),i.reach=Math.max(i.reach,r.length)}}for(let{nodes:r}of o.values())r.sort((s,i)=>s.stable.start-i.stable.start);let a=[];for(let r of t){let s=o.get(r.refName);if(!s)continue;let i=[],c=[],d=new Set,m,p=1/0,l=0,u=(r.start+r.end)/2,{nodes:h,reach:f}=s;for(let g=xt(h,r.start-f);g<h.length&&h[g].stable.start<r.end;g++){let w=h[g],x=w.stable.start,v=x+w.length;if(v<=r.start)continue;let y=n[w.id];d.add(w.id),l+=Math.min(v,r.end)-Math.max(x,r.start);let k=[],b=[];for(let S of r.exons){let M=Math.max(S.start,x),N=Math.min(S.end,v);if(N<=M)continue;let C=Tt(y,(M-x)/w.length,(N-x)/w.length);C.length===1&&C.push({...C[0]}),k.push(ye(C)),b.push(C)}k.length>0&&(i.push(...k),c.push({nodeId:w.id,d:k.join(""),stretches:b}));let L=Math.min(Math.max(u,x),v),R=Math.abs(L-u);if(R<p){p=R;let S=w.length?(L-x)/w.length:0;m=Tt(y,S,S)[0]}}m&&a.push({gene:r,exons:i.join(""),exonsByNode:c,nodeIds:d,at:m,covered:l/(r.end-r.start)})}return a}var ur="11.9.0";function _e(e,t,n={}){return{nodePositions:n.drawsRows?{}:e.nodePositions,deletions:t.bypassed,deletionRoutes:e.deletionRoutes,stranded:e.stranded,hiddenEdges:t.hidden}}var hr=(e,t)=>!!e.referencePath&&H(t).name===e.referencePath;function va(e,t){let n=H(t).name;return(e.paths??[]).filter(o=>H(o.name).name===n).sort((o,a)=>(o.start??0)-(a.start??0))}var fr=e=>new Map(e.nodes.map(t=>[t.id,t]));function Ma(e){let t=new Map;return e.edges.forEach((n,o)=>{t.set(`${n.from}>${n.to}`,o)}),{byId:fr(e),edgeAt:t}}function La(e,t,{byId:n,edgeAt:o}){let a=va(e,t),r=a[0];if(!r)return;let s=R=>n.get(R)?.length??0,i=R=>R.nodeIds.reduce((S,M)=>S+s(M),0),c=a.reduce((R,S)=>R+i(S),0),d=R=>{let S=Math.min(...R.map(M=>M.start??1/0));return Number.isFinite(S)?{start:S,end:Math.max(...R.map(M=>(M.start??0)+i(M)))}:void 0},m=d(a),p=m&&{contig:r.contig??Ve(H(t).name),...m},l=p?p.end-p.start:c,u=new Set,h=new Set,f=new Map,g=new Map,w=1,x=0;for(let R of a)p&&(x=Math.max(x,(R.start??0)-p.start)),R.nodeIds.forEach((S,M)=>{u.add(S);let N=(g.get(S)??0)+1;if(g.set(S,N),w=Math.max(w,N),M>0){let Xe=R.nodeIds[M-1],P=o.get(`${Xe}>${S}`)??o.get(`${S}>${Xe}`);P!==void 0&&h.add(P)}let C=s(S);f.has(S)||f.set(S,l>0?(x+C/2)/l:0),x+=C});let v=0,y=0,k;a.forEach((R,S)=>{if(k!==void 0&&R.start!==void 0&&R.start>k)for(let M of Rn(R.start-k,a[S-1].after,R.before))v+=M.cause==="missing"?M.bp:0,y+=M.cause==="unknown"?M.bp:0;k=R.start===void 0?void 0:R.start+i(R)});let b=hr(e,t),L=()=>{let R=b?[]:(e.paths??[]).filter(M=>hr(e,M.name));if(R.length===0)return;let S=d(R);return S?S.end-S.start:R.reduce((M,N)=>M+i(N),0)};return{name:t,reference:b,range:p,nodeIds:u,edgeIndexes:h,progress:f,passes:g,mostPasses:w,route:a.map(R=>R.nodeIds),steps:a.reduce((R,S)=>R+S.nodeIds.length,0),bp:c,referenceBp:L(),missingBp:v,unknownBp:y}}function gr(e,t,n,o){let a=new Map;for(let[r,s]of t.progress){let i=e.get(r),c=n.field==="progress"?s:o&&i?Hn(i,o):void 0;a.set(r,Un(n,c))}return a}function Na(e,t,n){let o=new Set,a=0,r=e.referencePath;if(!r||n.reference)return{reversed:o,bp:a};let s=e.pathVisits;if(!s)return{reversed:o,bp:a};let i=s.pathIndex(H(n.name).name),c=s.pathIndex(r);for(let d of n.progress.keys()){let m=t.get(d),p=m?s.slot(m.name):-1,l=p<0?-1:s.firstBy(p,i),u=p<0?-1:s.firstBy(p,c);l>=0&&u>=0&&s.reversed[l]!==s.reversed[u]&&(o.add(d),a+=m.length)}return{reversed:o,bp:a}}function $e(e,t,n){let o=Ma(e),a=new Set,r=t.filter(d=>!a.has(d.walk)&&a.add(d.walk)).flatMap(d=>{let m=La(e,d.walk,o);return m?[{walk:m,layer:d}]:[]}).sort((d,m)=>Number(m.walk.reference)-Number(d.walk.reference));if(r.length===0)return;let s=0,i=zn(r.map(({walk:d,layer:m})=>$t(m,d.reference,d.reference?0:s++,r.length===1))),c=r.map(({walk:d},m)=>{let p=i[m],{reversed:l,bp:u}=Na(e,o.byId,d);return{...d,encoding:p,colors:gr(o.byId,d,p,n),reversed:l,reversedBp:u}});return wr(c,n)}var Pa={field:"progress",scheme:"red"};function He(e,t,n,o){let a=fr(e);return t.walks.map(r=>{let s=n.find(c=>c.walk===r.name)?.color,i=$t({walk:r.name,color:{...Pa,...s}},r.reference,0);return wr([{...r,encoding:i,colors:gr(a,r,i,o)}],o)})}function wr(e,t){return{walks:e,referenceDomain:t?{start:t.start,end:t.start+t.span}:void 0,nodeIds:new Set(e.flatMap(n=>[...n.nodeIds])),edgeIndexes:new Set(e.flatMap(n=>[...n.edgeIndexes])),names:new Set(e.map(n=>n.name))}}var oe={..._t,width:1200,height:800,colorScheme:"auto",nodeWidth:"depth",contigThickness:6,connectorThickness:2};var br=[{value:"auto",label:"Auto"},{value:"uniform",label:"Uniform"},{value:"random",label:"Random"},{value:"rainbow",label:"Rainbow"},{value:"depth",label:"Depth"},{value:"node-length",label:"Node length"},{value:"stable-rank",label:"Stable rank"},{value:"reference-position",label:"Reference position"},{value:"grey",label:"Grey"}],Aa=br.map(e=>e.value);function We(e,t){return e!=="auto"?e:t?.anchoredBy?"reference-position":"uniform"}function yr(e,t,n){let o=n.region,a=n.colorDomain??o,r=n.walkRows,s=Te(t,{region:n.fitToDrawing?void 0:o,extent:r&&t.extent?he(r,n.walkRowPitch):void 0}),i=new Map(e.nodes.map(b=>[b.id,b])),c=We(n.colorScheme??oe.colorScheme,e),d=c==="reference-position"&&!t.tubeMap?Ne(e,a):void 0,m=Se(e,t.tubeMap?[]:Re(e),n.showDeletionEdges),p=n.walks??[],l=p.some(b=>b.color?.field==="reference")?d??Ne(e,a):void 0,u=p.length>0&&!t.tubeMap?$e(e,p,l):void 0,h=tt(n.facet),f=h.field&&u&&u.walks.length>1?He(e,u,p,l):void 0,g=h.field&&f?{panels:f,place:nt(f.map(b=>b.walks[0].name),h.field,h.domain)}:void 0,w=Ye(e.paths?.length?ve(e.paths):[]),x=n.referenceName??vt(e,o),v=n.contigThickness??oe.contigThickness,y=n.nodeWidth??oe.nodeWidth,k=u?.referenceDomain&&{...u.referenceDomain,name:x};return{bounds:s,nodeById:i,colorScheme:c,referenceRamp:d,drawnDeletions:m,layers:p,lift:u,facet:h,facets:g,labelOf:b=>w.get(b)??b,referenceName:x,keyText:b=>{let L=Po(b,k);return{note:L.delta+L.gaps+L.reversed,scale:L.scale}},contigThickness:v,nodeWidth:y,geometry:(b,L)=>Ke({..._e(t,m,{drawsRows:!!r}),graph:e,nodeById:i,colorScheme:c,contigThickness:v,connectorThickness:n.connectorThickness??oe.connectorThickness,drawPaths:!1,nodeWidth:y,linearLayout:n.linearLayout,highlight:b,axis:L,referenceRamp:d})}}var ft='font-family="Helvetica, Arial, sans-serif" font-size="11"',Ta=48,pe=18,xr=16,gt=16,Ga=32,Ea=22,Ia="rgb(160,160,160)",Rr="#1c1c22";function tn(e,t,n,o,a,r,s,i=1){let c=o.length>1?Ta:pe,d=o.length>1?`fill="url(#${e})"`:`fill="${o[0].color}"${i<1?` fill-opacity="${i}"`:""}`,m=o.length>1?`<linearGradient id="${e}">${o.map(l=>`<stop offset="${l.offset}" stop-color="${l.color}"/>`).join("")}</linearGradient>`:"";return{width:Math.max(c+5+(a.length+r.length)*se,(s?.length??0)*se),height:s?Ga:gt,markup:`${m}<g transform="translate(${t} ${n})" ${ft}><rect y="5" width="${c}" height="8" rx="2" ${d}/><text x="${c+5}" y="13"><tspan font-weight="bold">${Q(a)}</tspan>${Q(r)}</text>${s?`<text y="28">${Q(s)}</text>`:""}</g>`}}function Ca(e,t){return{width:pe+5+4*se,height:gt,markup:`<g transform="translate(${e} ${t})" ${ft}><rect x="1" y="4" width="${pe-2}" height="10" rx="4" fill="none" stroke="${Dt}" stroke-width="2"/><text x="${pe+5}" y="13">exon</text></g>`}}function Ba(e,t,n){let o=[6,9,12].map(a=>`<line y1="${a}" y2="${a}" x2="${pe}" stroke="#444" stroke-width="${Cn}"/>`).join("");return{width:pe+5+n.length*se,height:gt,markup:`<g transform="translate(${e} ${t})" ${ft}>${o}<text x="${pe+5}" y="13">${n}</text></g>`}}function Oa(e,t){let n=[],o=6,a=2,r=0;for(let s of e){let i=s(0,0);o>6&&o+i.width>t-6&&(o=6,a+=r+4,r=0),n.push(s(o,a).markup),o+=i.width+xr,r=Math.max(r,i.height)}return{markup:n,height:a+r}}function kr(e,t,n,o,a,r){return tn(e,t,n,Ht(o.encoding),a,r.note,r.scale)}function _a(e,t){return e.replaceAll(/([ML])(-?[\d.e-]+),(-?[\d.e-]+)/g,(n,o,a,r)=>`${o}${+(Number(a)*t.scaleX+t.translateX).toFixed(1)},${+(Number(r)*t.scaleY+t.translateY).toFixed(1)}`)}function $a(e,t,n,o,a){return`<rect x="${e-n/2}" y="${t-xe-At+2}" width="${n}" height="${xe+At*2-2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${Dt}"/><text x="${e}" y="${t}" font-family="Helvetica, Arial, sans-serif" font-size="${xe}" fill="${Rr}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${Q(o)}</tspan>${a?Q(a):""}</text>`}function nn(e,t,n={}){let o=n.width??oe.width,a=n.height??oe.height,r=n.walkRows,{bounds:s,nodeById:i,referenceRamp:c,layers:d,lift:m,facet:p,facets:l,labelOf:u,referenceName:h,keyText:f,contigThickness:g,nodeWidth:w,geometry:x}=yr(e,t,n),v=t.pixelRows??!1,y=c&&{start:c.start,end:c.start+c.span},k=n.genes?.length&&!t.tubeMap&&!r?Oe(e,n.genes,t.nodePositions):[],b=ze(e,i,g,w),L=0;function R(P,T,A,O){let _=[],X=So(Ro(k,b.halfWidthPx,P,$=>_a($,T)),{id:`exons${L++}`,width:A,height:O});X&&_.push(ie(X));let G=$=>({x:$.x*T.scaleX+T.translateX,y:$.y*T.scaleY+T.translateY}),E={width:A,height:O};for(let{item:$,x:re,y:J,w:Yr,text:zr}of Pn(Mo(k,G,g,vo(t.nodePositions,T)),E,Nn(E))){let Ur=G($.at).y+g/2;_.push(`<line x1="${re}" x2="${re}" y1="${J-xe-2}" y2="${Ur}" stroke="${Rr}" stroke-width="0.8" stroke-opacity="0.6"/>`,$a(re,J,Yr,$.gene.name,zr.slice($.gene.name.length)))}r&&_.push(ie(Ot(r,{...T,width:A,height:O,...n.walkRowPitch},{ramp:y,rowGenes:n.rowGenes})));let F=fe(r,t,n.walkRowPitch);for(let{label:$,y:re}of F){let J=re*T.scaleY+T.translateY;J>=0&&J<=O&&_.push(`<text x="6" y="${J+4}" ${ft} stroke="#fff" stroke-width="3" paint-order="stroke">${Q($)}</text>`)}return _.join("")}function S(P,T,A){let O=Ae(s,T,A,v,l?{padLeft:K,padTop:K,padRight:K,padBottom:K}:{});if(!O)return"";let _=ot(O.scale,v),{canvas:X,markup:G}=xo(T,A),E=new ko(X);E.uploadGeometry(x(P,_));let F={scaleX:_.scaleX,scaleY:_.scaleY,translateX:O.translateX,translateY:O.translateY};return E.updateTransform({...F,dpr:1}),E.render([1,1,1,1]),G()+R(P,F,T,A)}let M=[],N;if(l){let{panels:P,place:T}=l,A=et({count:T.count,bounds:s,pixelRows:v,width:o,room:a,columns:T.columns??p.columns});P.forEach((O,_)=>{let X=T.cells[_],G=X%A.columns*(A.width+Pe),E=Math.floor(X/A.columns)*(A.height+Qe+Pe),F=O.walks[0];M.push(kr(`key${_}`,G+6,E+2,F,u(F.name),f(F)).markup,`<svg x="${G}" y="${E+Qe}" width="${A.width}" height="${A.height}">${S(O,A.width,A.height)}</svg>`)}),N=A.total}else{let P=[];m&&(m.walks.forEach((G,E)=>{P.push((F,$)=>kr(`key${E}`,F,$,G,u(G.name),f(G)))}),P.push((G,E)=>tn("faded",G,E,[{offset:0,color:Ia}],"",`not on ${m.walks.length===1?u(m.walks[0].name):"these walks"}`,void 0,.3)),Bn(m.walks)&&P.push((G,E)=>Ba(G,E,On(m.walks)))),r?Ct(r,{ramp:y,genes:n.rowGenes?.size?n.rowGeneGaps:void 0}).forEach((E,F)=>{P.push(($,re)=>{let J=Bt([E],$,re,`rows-key-${F}`);return{width:J.width-xr,height:gt,markup:ie(J.tree)}})}):!m&&c&&P.push((G,E)=>tn("ramp",G,E,Ht({field:"reference",scheme:"rainbow"}),h?`${h} position`:"Reference position","",No(h,c.start,c.start+c.span))),k.some(G=>G.exonsByNode.length>0)&&P.push((G,E)=>Ca(G,E));let T=Oa(P,o);M.push(...T.markup);let A=P.length>0?Math.max(Qe,T.height):0,O=o-2*B,_=v||!(s.w>0)?s.h:s.h*O/s.w,X=Math.max(160,Math.min(a-A,Math.ceil(_+2*B)));M.push(`<svg y="${A}" width="${o}" height="${X}">${S(m,o,X)}</svg>`),N=A+X}let C=n.walkStrip;if(C&&!r&&!t.tubeMap){let P=Ie(C.rows,{width:o}),T=Bt(Ct(C.rows,{ramp:y,genes:qt(P,C.rowGenes,C.rowGeneGaps)}),6,N+P.height,"strip-key");M.push(`<line x1="0" x2="${o}" y1="${N+.5}" y2="${N+.5}" stroke="#ddd"/>`,`<svg y="${N}" width="${o}" height="${P.height}">${ie(Ot(C.rows,P,{ramp:y,rowGenes:C.rowGenes,idPrefix:"strip"}))}${ie(Jt(C.rows,P,new Set(d.map(A=>A.walk))))}</svg>`,ie(T.tree)),N+=P.height+Ea}let Xe=JSON.stringify({generator:`@jbrowse/bandage-core@${ur}`,...n.spec===void 0?{}:{spec:n.spec}});return`<svg xmlns="http://www.w3.org/2000/svg" width="${o}" height="${N}" viewBox="0 0 ${o} ${N}"><metadata>${Q(Xe)}</metadata><rect width="${o}" height="${N}" fill="#fff"/>${M.join("")}</svg>
-`}var Ha=.9;function Fe(e,t){return e+2>=t||e>=Ha*t}var Wa=50;function on(e,t,n,o=[]){let a=new Map(e.nodes.map(s=>[s.name,s])),r=[];for(let s of t){let i=[],c=1/0,d=-1/0,m=1/0,p=[],l=ce(s);for(let[f,g]of l.entries()){let w=a.get(g),x=w&&n[w.id];if(!(!w||!x?.length)&&!(s.key?f===0||f===l.length-1:I(w)&&(w.stable.start<s.start||w.stable.start>=s.end))){p.push(w.id),i.push(ye(x.length===1?[x[0],x[0]]:x));for(let v of x)c=Math.min(c,v.x),d=Math.max(d,v.x),m=Math.min(m,v.y)}}if(p.length===0)continue;let u={x:(c+d)/2,y:m},h=s.covering===!0||Fe(p.length,e.nodes.length);r.push({bubble:s,...so(s,o),path:i.join(""),labelAt:u,members:p.length,nodeIds:p,whole:h,tick:!h&&!s.partial&&s.longestAlleleLength<Wa})}return r}function De(e,t){let n=new Set(t),o=e.nodes.filter(c=>n.has(c.name)),a=new Set(o.map(c=>c.id)),r=new Map(e.nodes.map(c=>[c.id,c.length])),s=new Map,i=e.paths?.flatMap(c=>{let d=c.nodeIds.findIndex(l=>a.has(l));if(d<0)return[];let m=c.nodeIds.filter(l=>a.has(l));s.set(c.name,{first:d,nodeIds:m});let p=c.nodeIds.slice(0,d).reduce((l,u)=>l+(r.get(u)??0),0);return[{...c,nodeIds:m,...c.start===void 0?{}:{start:c.start+p}}]});return{name:e.name,nodes:o,edges:e.edges.filter(c=>a.has(c.from)&&a.has(c.to)),...i?.length?{paths:i}:{},anchorPaths:vn(e,s),pathVisits:e.pathVisits,anchoredBy:e.anchoredBy,referencePath:e.referencePath}}function rn(e,t,n,o){let a=e.get(t);e.set(t,{min:Math.min(a?.min??1/0,n.min+o),max:Math.max(a?.max??-1/0,n.max+o),n:Math.min(ao,n.n+(a?.n??0))})}function Sr(e){if(!e.nodes.some(I))return[];let t=new Map(e.nodes.map(l=>[l.id,l])),n=Vt(e),o=new Map(n.map((l,u)=>[l,u])),a=new Int32Array(n.length+1),r=new Map,s=new Set;for(let l of e.edges){let u=o.get(l.from),h=o.get(l.to);if(u===void 0||h===void 0||u===h)continue;s.add(`${l.from}>${l.to}`).add(`${l.to}>${l.from}`);let[f,g]=u<h?[u,h]:[h,u];a[f+1]++,a[g]--;let[w,x]=u<h?[l.from,l.to]:[l.to,l.from];yn(r,w,x)}for(let l=1;l<a.length;l++)a[l]+=a[l-1];let i=e.nodes.filter(I).sort((l,u)=>l.stable.start-u.stable.start),c=new Set([i[0].id,i.at(-1).id]),d=i.map(l=>[l,o.get(l.id)]).filter(([l,u])=>c.has(l.id)||a[u]===0).sort(([l,u],[h,f])=>u-f||l.stable.start-h.stable.start),m=an(e,d.map(([l])=>l.id)),p=[];for(let l=0;l+1<d.length;l++){let[u,h]=d[l],[f,g]=d[l+1],w=n.slice(h+1,g);if(w.length===0)continue;let x=new Map([[u.id,{min:0,max:0,n:1}]]);for(let S of[u.id,...w]){let M=x.get(S);if(M)for(let N of r.get(S)??[])o.get(N)>g||rn(x,N,M,N===f.id?0:t.get(N).length)}let v=sn(e,t,m,u.id,f.id,()=>x.get(f.id)??{min:0,max:0,n:0}),y=u.stable.start+u.length,k=f.stable.start,b=[u.id,...w.filter(S=>I(t.get(S))),f.id],L=b.some((S,M)=>M>0&&!s.has(`${b[M-1]}>${S}`)),R=k-y;p.push(cn({refName:u.stable.refName,start:y,end:k},[u,...w.map(S=>t.get(S)),f],L&&!v.routes?{...v,min:R,max:R}:v,L||v.walksLeave))}return p}function an(e,t){let n=e.paths;if(!n)return;let o=new Map;for(let a of t)o.set(a,new Int32Array(n.length).fill(-1));return n.forEach((a,r)=>{let s=a.nodeIds;for(let i=0;i<s.length;i++){let c=o.get(s[i]);c?.[r]===-1&&(c[r]=i)}}),o}function sn(e,t,n,o,a,r){if(!n)return{...r(),walksLeave:!1};let s=[],i=1/0,c=-1/0,d=0,m=n.get(o),p=n.get(a);e.paths.forEach((u,h)=>{let f=m[h],g=p[h];if(f<0||g<0){(f>=0||g>=0)&&d++;return}let w=u.nodeIds,x=Math.min(f,g)+1,v=Math.max(f,g),y=g<f?b=>w[v-1-b]:b=>w[x+b],k=s.find(b=>b.steps.length===v-x&&b.steps.every((L,R)=>L===y(R)));if(!k){let b=Array.from({length:v-x},(R,S)=>y(S)),L=0;for(let R of b)L+=t.get(R)?.length??0;k={steps:b,bp:L,walks:[]},s.push(k)}k.walks.push(u.name),i=Math.min(i,k.bp),c=Math.max(c,k.bp)});let l=d>0;return s.length?{min:i,max:c,n:s.length,routes:s,walksLeave:l}:{...r(),walksLeave:l}}function cn(e,t,{min:n,max:o,n:a,routes:r},s){return{...e,segmentCount:t.length,pathCount:a,inversion:!1,shortestAlleleLength:n,longestAlleleLength:o,segments:t.map(i=>i.name).join(","),shortestAllele:void 0,longestAllele:void 0,partial:s,routes:r}}function Fa(e,t){let n=e.nodes.length*2,o=new Set,a=[],r=new Int32Array(n);for(let d of e.edges){let m=t.get(d.from),p=t.get(d.to);if(m===void 0||p===void 0)continue;let l=ke(d),u=m*2+(l.from==="end"?1:0),h=p*2+(l.to==="end"?1:0),f=Math.min(u,h)*n+Math.max(u,h);o.has(f)||(o.add(f),a.push(u,h),r[u]++,u!==h&&r[h]++)}let s=new Int32Array(n+1);for(let d=0;d<n;d++)s[d+1]=s[d]+r[d];let i=new Int32Array(s[n]),c=s.slice(0,n);for(let d=0;d<a.length;d+=2){let m=a[d],p=a[d+1];i[c[m]++]=p,m!==p&&(i[c[p]++]=m)}return{offset:s,next:i}}function Da(e,t,n){let o=new Int32Array(e),a=new Uint8Array(e*2),r=new Int32Array(e*2),s=new Int32Array(e),i=[],c=0;return d=>{let m=d>>1;c++,i.length=0;let p=0,l=0,u=0,h,f=g=>{a[g]||(a[g]=1,p++,i.push(g))};f(d),r[l++]=d;e:for(;l>0;){let g=r[--l],w=g>>1;if(o[w]=c,w!==m&&(s[u++]=g),a[g]&&(a[g]=0,p--),t[g]===t[g+1])break;for(let x=t[g];x<t[g+1];x++){let v=n[x],y=v>>1;if(y===m)break e;if(f(v^1),o[y]===c)continue;let k=!0;for(let b=t[v];b<t[v+1];b++)if(o[n[b]>>1]!==c){k=!1;break}k&&(r[l++]=v^1)}if(l===1&&p===1){u>0&&(h={source:d,sink:r[0],inside:s.slice(0,u)});break}}for(let g of i)a[g]=0;return h}}function Xa(e){return{source:e.sink^1,sink:e.source^1,inside:e.inside.map(t=>t^1).reverse()}}var Lr=new Intl.Collator(void 0,{numeric:!0});function dn(e,t){return I(e)&&I(t)&&e.stable.refName===t.stable.refName}function vr(e,t){let n=t[e.source>>1],o=t[e.sink>>1],a=dn(n,o)?n.stable.start-o.stable.start:0,r=((e.sink^1)&1)-(e.source&1);return(a||r||Lr.compare(n.name,o.name))<0}function Mr(e){return[e.source>>1,...Array.from(e.inside,t=>t>>1),e.sink>>1]}function Va(e){let{nodes:t}=e,n=new Map(t.map((c,d)=>[c.id,d])),{offset:o,next:a}=Fa(e,n),r=Da(t.length,o,a),s=new Map;for(let c=0;c<t.length*2;c++){let d=r(c);if(!d)continue;let m=d.source>>1,p=d.sink>>1,l=Math.min(m,p)*t.length+Math.max(m,p);(vr(d,t)||!s.has(l))&&s.set(l,d)}return{found:[...s.values()].map(c=>vr(c,t)?c:Xa(c)),offset:o,next:a}}function ja(e,t,n,o){let a=o.sink>>1,r=new Map([[o.source>>1,{min:0,max:0,n:1}]]);for(let s of[o.source,...o.inside]){let i=r.get(s>>1);if(i)for(let c=t[s];c<t[s+1];c++){let d=n[c]>>1;rn(r,d,i,d===a?0:e[d].length)}}return r.get(a)??{min:0,max:0,n:0}}function pn(e,t){let{nodes:n}=e,{found:o,offset:a,next:r}=Va(e),s=o.map(h=>Fe(h.inside.length,n.length)),i=o.map(Mr),c=new Map;i.forEach((h,f)=>{for(let g of h)bn(c,g,f)});let d=(h,f)=>c.get(h.inside[0]>>1).some(g=>g!==f&&!s[g]&&i[g].length>i[f].length&&i[f].every(w=>c.get(w).includes(g))),m=h=>t!==void 0||dn(n[h.source>>1],n[h.sink>>1]),p=o.filter((h,f)=>!s[f]&&m(h)&&!d(h,f)),l=new Map(n.map(h=>[h.id,h])),u=an(e,p.flatMap(h=>[n[h.source>>1].id,n[h.sink>>1].id]));return p.map(h=>{let f=n[h.source>>1],g=n[h.sink>>1],w=sn(e,l,u,f.id,g.id,()=>ja(n,a,r,h)),x=dn(f,g);return{...cn({refName:x?f.stable.refName:t.refName,start:x?f.stable.start+f.length:t.start,end:x?g.stable.start:t.end},Mr(h).map(v=>n[v]),w,w.walksLeave),key:`${f.name}>${g.name}`,...x?{}:{offReference:!0}}}).sort((h,f)=>h.start-f.start||h.end-f.end||Lr.compare(h.key,f.key))}function wt(e,t){let n=e.nodes.length,o=Sr(e);if(o.length===0){let a=pn(e,t);return t?[...a,{...t,covering:!0}]:a}return o.flatMap(a=>Fe(a.segmentCount-2,n)?[...pn(a.segmentCount===n?e:De(e,ce(a)),a),{...a,covering:!0}]:[a])}function ln(e,t,n){if(t==="uniform"||t==="grey")return;let o=Wn(e,n);return new Map(e.nodes.map((a,r)=>[a.id,_n(Fn(a,r,t,o))]))}var bt=JBrowseExports["@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"];var Nr=bt&&bt.__esModule?bt.default:bt;var mn={paths:!1,bubbles:!1,deletions:!0,genes:!0,referenceStrip:!0,walkStrip:!1};function Pr(e){let t=z(e)?e:{};return new Set(Object.keys(mn).filter(n=>t[n]??mn[n]))}function Dh(e,t,n){let{[t]:o,...a}=z(e)?e:{};return n===mn[t]?a:{...a,[t]:n}}var un={depth:"depth",length:"node-length",rank:"stable-rank",position:"reference-position"},Ar=Object.fromEntries(Object.entries(un).map(([e,t])=>[t,e]));function Tr(e){if(e==="grey"||e==="uniform")return e;if(z(e)){let{field:t,scheme:n}=e;if(t==="id")return n==="rainbow"?"rainbow":"random";if(typeof t=="string"&&t in un)return un[t]}return"auto"}function Gr(e){return z(e)&&typeof e.domainMin=="number"&&typeof e.domainMax=="number"?{start:e.domainMin,end:e.domainMax}:void 0}function jh(e,t){return e==="grey"||e==="uniform"?e:e==="random"?{field:"id",scale:"categorical"}:e==="rainbow"?{field:"id",scheme:"rainbow"}:e==="reference-position"&&t?{field:"position",domainMin:t.start,domainMax:t.end}:Ar[e]?{field:Ar[e]}:{}}var Er=6;function hn(e){return typeof e=="number"?{width:"uniform",px:e}:z(e)?{width:e.field==="depth"?"depth":"uniform",px:typeof e.value=="number"?e.value:Er}:{width:"depth",px:Er}}function Uh(e,t){return e==="depth"?{field:"depth",value:t}:t}function Ya(e,t,n){let o=Mn(e,t);return o?Nt(o,n):void 0}function Ir(e){try{return e()}catch{return}}function Cr(e){let t=new Map;for(let n of e.nodes)t.set(n.id,n);return t}function Br(e,t,n){return t&&n?It({nodeId:e,nodeById:t,neighbors:n}):void 0}var Or=ro.views(e=>({sessionTrack(t){return U(e).tracks.find(n=>n.trackId===t)},get grammar(){return{}},get hasPendingSource(){return!1},get canRetryLoad(){return!1},get sourceTrack(){return Ir(()=>gn(e).configuration)},get containingView(){return Ir(()=>yt(e))}})).views(e=>{let t=r=>Ln(r,{equals:(s,i)=>JSON.stringify(s)===JSON.stringify(i)}),n=t(()=>Gr(e.grammar.color)),o=t(()=>tt(e.grammar.facet)),a=t(()=>{let r=uo(e.grammar.facet);return r&&r.field!=="walk"&&r.field!=="sample"?r:void 0});return{get chosenLayoutMode(){return e.grammar.layoutMode??"force"},get chosenColorScheme(){return Tr(e.grammar.color)},get statedColorDomain(){return n.get()},get chosenHover(){return e.grammar.hover??"nodes"},get nodeWidth(){return hn(e.grammar.size).width},get contigThickness(){return hn(e.grammar.size).px},get layerSet(){return Pr(e.grammar.layers)},get drawPaths(){return this.layerSet.has("paths")},get showBubbles(){return this.layerSet.has("bubbles")},get showDeletionEdges(){return this.layerSet.has("deletions")},get showGenes(){return this.layerSet.has("genes")},get showReferenceStrip(){return this.layerSet.has("referenceStrip")},get walkStrip(){return this.layerSet.has("walkStrip")},get facetSetting(){return o.get()},get walkRowGroupBy(){return a.get()},get walkRowSamples(){let r=e.grammar.rows?.kept;return Array.isArray(r)?r:void 0},get hoverLightsEverything(){return this.chosenHover==="everything"},get litNode(){return this.chosenHover==="off"?null:e.hoveredNode}}}).views(e=>({get paneWidth(){return yt(e).width},get paneMeasured(){return!0},get drawnGraph(){return e.layoutResult?.tubeMap?.graph??e.graph}})).views(e=>({get nodeById(){return e.drawnGraph&&Cr(e.drawnGraph)},get nodeLengths(){let t=new Map;for(let n of e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get legendAtRest(){return e.hoveredNode===null&&e.hoveredRowWalks.length===0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return no(e)},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!this.geometryPainted)},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Yt(e.chosenLayoutMode,e.graph):!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?ve(t):[]},get effectiveDrawPaths(){return e.drawPaths&&je(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){let t=e.openBubbles.at(-1);return t&&!t.offReference&&t.end>t.start?{start:t.start,end:t.end}:e.statedColorDomain??e.graphRegion},get drawnReferenceRamp(){let t=e.drawnGraph;return t?Ne(t,this.rampDomain):void 0},get walkRamp(){return e.walkLayers.some(t=>t.color?.field==="reference")?this.drawnReferenceRamp:void 0},get modeDrawsNodes(){return Y(e.chosenLayoutMode).drawsNodes},get liftedWalkLayers(){return e.walkLayers.length>0||!this.modeDrawsNodes?e.walkLayers:e.hoveredRowWalks.map(t=>({walk:t}))},get walkLift(){let{graph:t}=e,n=this.liftedWalkLayers;return t&&!e.walkCut&&n.length>0&&!e.layoutResult?.tubeMap?$e(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facetSetting.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?He(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!Qn.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Ye(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(Kn))},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":We(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return 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?wt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>wt(De(t,ce(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(ce(t)),a=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),r=new Set;return n.edges.forEach((s,i)=>{a.has(s.from)&&a.has(s.to)&&r.add(i)}),{walks:[],nodeIds:a,edgeIndexes:r,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>at(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,a=this.openBubbleFocus;return o?!n.some(r=>o.nodeIds.has(r)):!!a&&!this.bubbleIsOpen(t)&&!n.every(r=>a.nodeIds.has(r))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(st));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(st(o))&&n.add(st(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Tn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?Yo(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?V(t,"trackId"):void 0},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:V(n,"name"),adapterType:V(n,"adapter").type,assemblies:Qt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Zt(U(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>ct.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>_o.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return $o(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return dt(e.geneTrackChoices,e.geneTrackId)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?St(e.graph):void 0},get cutWalkRows(){let t=e.walkCut?.walkRowRuns;return t?Nt(t):e.graph?ue(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=U(e),o=n.has(t)?n.get(t):void 0,a=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(s=>a[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=Ho(t,e.geneTrack?.trackId);return n.length?new Nr({filters:n,jexl:wn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Wo(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,a=e.drawsLoadedReference||n!==void 0&&Mt(t,[n])!==void 0;return t&&o&&a?Lt(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?Z(e.drawnGraph):void 0},get nodeInk(){return ze(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?Re(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?Ya(n,t,t.unit):ue(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[a,...r]=Fo([o.reference,...o.rows],t?.calls);return{...o,reference:a,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&Sn(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=yo(t,n),a=(e.graph?.paths??[]).map(r=>H(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:wo(a.map(o)),unvalued:a.some(r=>o(r)==="")}},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,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows;return t&&Me(t.rows,e.walkRowSamples)},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?ho(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 drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ge(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?Oe(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){Ge(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:on(e.graph,e.bubbles,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 ot(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?Se(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 referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!I(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?ln(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!je(n.length)||n.some(a=>a.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],a=this.tubeColorKind,r=e.tubeMapColoring;return a==="value"&&r?bo(o,t.referencePath,r.valueOf,r.palette):a==="tinted"?Ft(o,t.referencePath,go):a==="role"?Ft(o,t.referencePath):n},fadeUnhovered(t,n,o){let a=new Set(e.hoveredRowWalks);return a.size>0?t.map((r,s)=>{let i=n[s]?.name??"";return a.has(i)||o!==void 0&&H(i).name===o?r:Ue}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return Br(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&Cr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&Z(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&je(t.length)&&!t.some(o=>o.members)?ve(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?Br(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var _r=Or.views(e=>({get host(){let t=e.containingView;return Xo(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?q(t):[];return t?cr(t,{maxGap:n.length>0?Rt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=U(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,s])=>[s,r])),a=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>a(o.get(r))??a(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(ct.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let a=dt(o,"");return a?[[n,a]]:[]}))}})).views(e=>({get launchableAssemblies(){return dr(mr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Be({views:[...U(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?sr(n):void 0,a=o?Ce(e.assemblyResolver,o):void 0,r=e.graphRegion,s=r?e.nodeSpan(t):void 0,i=r&&s?{sample:r.assemblyName,haplotype:void 0,refName:r.refName,...s}:void 0;return{own:o&&a?{location:en(o),assembly:a}:void 0,reference:r&&i?{location:en(i),assembly:r.assemblyName}:void 0,highlight:r&&i?{location:i,assembly:r.assemblyName}:void 0}}}));var $r=_r.views(e=>({get walkStripShown(){return zt({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:Me(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ie(t,{width:e.paneWidth})},get cutsWholeWalks(){return Ut(Y(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?Kt(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:Ce(e.assemblyResolver,o),span:{refName:n.contig,...Je(n,t.bp)}}},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:it(e.nodePositions?.[t],e.toScreen)}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,a=0;for(let r of t.rows){if(!r.axis){a++;continue}let{assembly:s,span:i}=e.rowLocation(r,r.axis),c=s?e.geneTracksByAssembly.get(s):void 0;if(!s||!c){o++;continue}n.push({row:r.name,trackId:c.trackId,region:{assemblyName:s,...i}})}return{reads:n.slice(0,Wt),gaps:{untracked:o,unplaced:a,unread:Math.max(0,n.length-Wt)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let{sample:a,haplotype:r,assembly:s,span:i}=e.rowLocation(o,o.axis);return{label:o.label,assembly:t===0?e.graphRegion?.assemblyName:s,location:{sample:a,haplotype:r,...i}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?Vn([t.reference,...t.rows],n):void 0}}));var Hr=$r.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&Y(e.drawnLayoutMode??e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostBpFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?jo(t,n):void 0}})).views(e=>({get hostFrame(){return e.hostPlacesX?e.hostBpFrame:void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?po(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t?io(t):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap;return t?.coarse?co(t,t.coarse.deviations):[]},get tubeMapConnectedBoxes(){let t=this.tubeMapReference,{layoutResult:n}=e;return t&&!n?.referenceAxis&&!n?.tubeMapPanels?[...t.values()].flat():void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes&&!e.layoutResult?.tubeMapPanels?To(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;if(!e.showReferenceStrip||!e.referenceStripApplies||!t)return[];let n=Co(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}),o=e.walkLift?void 0:e.openBubbleFocus;return o?n.map(a=>o.nodeIds.has(a.node)?a:{...a,colors:[Ue],faded:!0}):n}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.hostBpFrame!==void 0},get referenceStripOverhangs(){let t=e.hostBpFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:o}=Bo(e.referenceStripBlocks,t,e.paneWidth);return n>0||o>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=e.hoveredNode===null?e.hoveredBubble:null;if(t&&!t.offReference){let a=e.bubbleHalos.find(r=>at(r.bubble,t));return{start:t.start,end:t.end,anchor:a?e.toScreen(a.labelAt):void 0}}let n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeSpan(n);return o&&n!==null?{...o,anchor:it(e.nodePositions?.[n],e.toScreen)}:void 0},referenceStripNodeAt(t,n){let o=e.hostBpFrame;return e.referenceStripShown&&o?Oo(e.referenceStripBlocks,o,t,n):void 0},get referenceStripZonePx(){return e.referenceStripShown?Io:0}}));var za=3e3,Ua=350,Ka=34;function Ja(e){let t=[0];for(let n=1;n<e.length;n++)t.push(t[n-1]+Math.hypot(e[n].x-e[n-1].x,e[n].y-e[n-1].y));return t}function qa(e,t){if(e.length===1||t===1)return Array.from({length:t},()=>({...e[0]}));let n=Ja(e),o=n.at(-1),a=[],r=1;for(let s=0;s<t;s++){let i=o*s/(t-1);for(;r<e.length-1&&n[r]<i;)r++;let c=n[r]-n[r-1],d=c>0?(i-n[r-1])/c:0,m=e[r-1],p=e[r];a.push({x:m.x+(p.x-m.x)*d,y:m.y+(p.y-m.y)*d})}return a}var Za=400,Wr=1.8,Qa=.1;function _g(e,t,n,o,a){let r=y=>({x:(y.x*t.scaleX+t.translateX-o.translateX)/o.scaleX,y:(y.y*t.scaleY+t.translateY-o.translateY)/o.scaleY}),s={};for(let[y,k]of Object.entries(n)){let b=e[y];b?.length&&k.length&&(s[y]=qa(b.map(r),k.length))}let i=new Map,c=(y,k)=>{let b=i.get(y);b?b.push(k):i.set(y,[k])};for(let y of a){let{from:k,to:b}=y;if(k!==b&&n[k]?.length&&n[b]?.length){let L=ke(y);c(k,{id:b,side:L.to}),c(b,{id:k,side:L.from})}}let d=new Map,m=y=>d.get(y.id)??(y.side==="start"?s[y.id][0]:s[y.id].at(-1)),p=Object.keys(s),l=[];for(let y of p)for(let k of i.get(y)??[]){if(s[k.id]||d.has(k.id))continue;let b=i.get(k.id).find(L=>L.id===y);d.set(k.id,{...m(b)}),p.push(k.id),l.push(k.id)}let u=new Map(l.map((y,k)=>[y,k])),h=new Float64Array(l.map(y=>d.get(y).x)),f=new Float64Array(l.map(y=>d.get(y).y)),g=new Float64Array(l.length),w=new Float64Array(l.length),x=l.map((y,k)=>i.get(y).flatMap(b=>{let L=u.get(b.id);if(L===void 0){let R=m(b);return g[k]+=R.x,w[k]+=R.y,[]}return[L]})),v=l.map(y=>i.get(y).length);for(let y=0;y<Za;y++){let k=0;for(let b=0;b<l.length;b++){let L=g[b],R=w[b];for(let N of x[b])L+=h[N],R+=f[N];let S=Wr*(L/v[b]-h[b]),M=Wr*(R/v[b]-f[b]);k=Math.max(k,Math.abs(S*o.scaleX)+Math.abs(M*o.scaleY)),h[b]+=S,f[b]+=M}if(k<Qa)break}l.forEach((y,k)=>{s[y]=n[y].map(()=>({x:h[k],y:f[k]}))});for(let[y,k]of Object.entries(n))s[y]??=k.map(b=>({...b}));return s}function es(e,t){let n=0,o=1/0;return e.forEach((a,r)=>{let s=(a.x-t.x)**2+(a.y-t.y)**2;s<o&&(o=s,n=r)}),n}function $g(e,t,n,o){let a=(r,s)=>{let i=n[r],c=o[r];if(!i||!c||c.length===0)return{x:0,y:0};let d=es(c,s);return{x:i[d].x-c[d].x,y:i[d].y-c[d].y}};return Object.fromEntries(Object.entries(e).map(([r,s])=>{let i=t[Number(r)],c=a(i?.from??"",s[0]),d=a(i?.to??"",s.at(-1));return[r,s.map((m,p)=>{let l=s.length>1?p/(s.length-1):0;return{x:m.x+c.x+(d.x-c.x)*l,y:m.y+c.y+(d.y-c.y)*l}})]}))}function Fr(e,t,{ids:n,alpha:o}){let a=(r,s)=>{for(let i=0;s&&i<s.count;i++){let c=r[s.start+i];c.color=$n(c.color,o)}};for(let r of n)a(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:s},i)=>{(n.has(r)||n.has(s))&&(a(e.edgeCurves,e.edgeCurveRuns.get(i)),a(e.arrows,e.arrowRuns.get(i)))})}function ts(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function Hg(e,t,n,o){return!(e.referenceAxis||t.referenceAxis||e.pixelRows||t.pixelRows||t.tubeMap||o||n>za)}function Wg(){return typeof requestAnimationFrame<"u"&&!("matchMedia"in window&&window.matchMedia("(prefers-reduced-motion: reduce)").matches)}function Fg(e,t,n){let o={frame:0,finish:()=>{e(1)}},a=0,r=performance.now(),s=()=>{if(!t()){n();return}let i=performance.now();a+=Math.min(i-r,Ka),r=i;let c=Math.min(1,a/Ua);e(ts(c)),c<1?o.frame=requestAnimationFrame(s):n()};return o.frame=requestAnimationFrame(s),o}function Dg(e,t,n,o){for(let[a,r]of Object.entries(e)){let s=t[a],i=n[a];!s||!i||r.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 ns=8,os=19,Dr=Pe+os,rs=48;function as(e,t,n){if(!(!e||!t))return qe(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var dw=Hr.views(e=>({get paneCeiling(){return Math.max(rt,e.paneHeight??Jn)},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)*lo;return Ze(t.rows.length+1,n-this.fitPadTopBase-B-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?fo(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return as(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=fe(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,a)=>({...o,y:t.rowY(a)})):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,An(n.label,0).x1+6),B)},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?he(n,this.walkRowPitch):void 0;return t?Te(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,a=o?t.reference:t.rows.find(r=>r.name===n);return a?{label:a.label,readout:Dn(a,o?void 0:t.reference,t.unit,a.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,a=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!a||!r)return;let s=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][s],c=r.rowY(s)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=a.barPx/2+2&&d>=0&&d<=i.bp?s:void 0},get fitPadTopBase(){let t=Eo(e.tubeMapGenes);return B+Math.max(0,t-1)*Go+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let a=this.fitPadTopBase,r=this.fitRoom,s=m=>(e.paneWidth-this.fitPadLeft-m)/t.w,i=m=>e.pixelRows?t.h+m+B<=r?1/0:0:(r-m-B)/t.h,c=Math.min(s(n+2*ee),i(a));return Math.min(s(B),i(a+o+ee))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ee:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(B,e.legendSize.width+2*ee):B},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(Zn/o,(this.paneCeiling-this.fitPadTop-B)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?nt(t.map(a=>a.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?et({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-Dr)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ee+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-rs?t+2*ee:ns},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(rt,o.total+Dr);let a=Math.max(rt,e.legendSize.height+2*ee+e.referenceStripZonePx),r=this.fitPads,s=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(a,t.h+s));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(a,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:K,top:K,right:K,bottom:K}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:B}},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,a=this.fitPads;return t?Ae(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:a.left,padTop:a.top,padRight:a.right,padBottom:a.bottom}):void 0}})).views(e=>({viewportToBuild(){return Yn(oo(e),to)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,eo]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=Do();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]:qn)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:a,layoutResult:r,deletionDrawing:s}=e;if(!o||!a||!r||!s)return;Ge(e.viewportDirty,e.positionsVersion);let i=Pt(()=>e.viewportToBuild()),c=Ke({..._e(r,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:Pt(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Fr(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return Lo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Ao(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:`${Y(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?nn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps}}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var fn=W(D("path",{d:"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z"}),"LineStyle");var Xr=W(D("path",{d:"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z"}),"CompareArrows");var Vr=W(D("path",{d:"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2"}),"HighlightAlt");var ss="Linear genome view",is="Linear synteny view",cs="No synteny track in this session aligns these assemblies";function jr({label:e,icon:t,entries:n,entryLabel:o,onSelect:a,disabledHelpText:r,nameTheOnlyEntry:s=!0}){let[i]=n,c=r?[{label:e,icon:t,disabled:!0,disabledHelpText:r,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:s?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:a(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(d=>({label:o(d),onClick:a(d)}))}]}function vw({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:a}){let r=n[0]?.coverage??e.length;return[...jr({label:ss,icon:fn,entries:t,entryLabel:s=>`${s.sample} ${ne(s)}`,onSelect:s=>()=>{o({location:s,assembly:s.sample})}}),...e.length>=2?jr({label:`${is} (${r} assemblies)`,icon:Xr,entries:n,entryLabel:s=>s.coverage<r?`${s.name} (${s.coverage} of ${r})`:s.name,nameTheOnlyEntry:!1,disabledHelpText:cs,onSelect:s=>()=>{a(s.trackId)}}):[]]}function Mw({own:e,reference:t,highlight:n,onShowLinear:o,onHighlight:a}){let r=[e?{label:`Open in ${e.assembly} \u2014 ${ne(e.location)}`,target:e}:void 0,t&&t.assembly!==e?.assembly?{label:`Open in ${t.assembly} \u2014 around this node`,target:t}:void 0].filter(s=>s!==void 0);return[...a&&n?[{label:`Highlight in ${n.assembly}`,icon:Vr,onClick:()=>{a(n)}}]:[],...r.map(({label:s,target:i})=>({label:s,icon:fn,onClick:()=>{o(i)}}))]}var Aw=W(D("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var Iw=W(D("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6"}),"Settings");var _w=W(D("path",{d:"M12 4.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5M12 17c-2.76 0-5-2.24-5-5s2.24-5 5-5 5 2.24 5 5-2.24 5-5 5m0-8c-1.66 0-3 1.34-3 3s1.34 3 3 3 3-1.34 3-3-1.34-3-3-3"}),"Visibility");export{W as a,Qo as b,ut as c,pa as d,Y as e,Ut as f,fa as g,ga as h,wa as i,Jt as j,qt as k,ne as l,ba as m,sr as n,z as o,Ra as p,Zt as q,Lc as r,Qt as s,Nc as t,Pc as u,Ac as v,br as w,_w as x,_g as y,$g as z,Hg as A,Wg as B,Fg as C,Dg as D,ln as E,Xo as F,us as G,Jr as H,hs as I,ea as J,Yo as K,Dh as L,jh as M,Uh as N,ns as O,os as P,Dr as Q,dw as R,fn as S,vw as T,Mw as U,Aw as V,Iw as W};
-//# sourceMappingURL=chunk-GRTN25B6.js.map