jbrowse-plugin-graphgenomeviewer 8.4.0 → 8.5.0

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

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=AddTrackWorkflow-JAIB6H2T.js.map
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+//# sourceMappingURL=AddTrackWorkflow-IOPTETLH.js.map

package/dist/chunks/AddTrackWorkflow-IOPTETLH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["jbrowse-host:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tss-react\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tss-react\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport {\n  addTrackFromWidget,\n  getEnv,\n  getSession,\n  makeTrackId,\n} from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot, isAlive } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  GRAPH_INDEX_FIELDS,\n  buildTrackConfig,\n  parseHaplotypes,\n} from './buildTrackConfig'\nimport { readGraphManifest } from './graphManifest'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'RgfaTabixWalks',\n  'GbzBaseSyntenyAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [readsLoc, setReadsLoc] = useState<FileLocation>()\n  const gbz = choice === 'GbzBaseSyntenyAdapter'\n  const walks = choice === 'RgfaTabixWalks'\n  const [sample, setSample] = useState('')\n  const [haplotypes, setHaplotypes] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n  const [submitting, setSubmitting] = useState(false)\n\n  async function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    setError(undefined)\n    setSubmitting(true)\n    const manifest =\n      choice === 'RgfaTabixAdapter'\n        ? await readGraphManifest(loc, getEnv(model).pluginManager)\n        : undefined\n    setSubmitting(false)\n    if (!isAlive(model) || !model.assembly) {\n      return\n    }\n    try {\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          readsLoc: gbz ? readsLoc : undefined,\n          manifest,\n          assembly: model.assembly,\n          sample,\n          haplotypes: walks ? parseHaplotypes(haplotypes) : undefined,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n            setIndexLoc(undefined)\n            setError(undefined)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name={GRAPH_INDEX_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      {gbz ? (\n        <FileSelector\n          location={readsLoc}\n          name=\"Path to reads aligned to the graph as GAF (optional; a .gz is read by the .tbi beside it)\"\n          rootModel={rootModel}\n          setLocation={setReadsLoc}\n        />\n      ) : null}\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText={\n          gbz\n            ? \"Optional. The graph's sample for this assembly, e.g. GRCh38 where the assembly is hg38; leave blank when they share a name or the graph has one reference sample\"\n            : walks\n              ? 'Optional. The PanSN sample this assembly is in the graph; blank takes it from the file name, GRCh38 in chr22.GRCh38.walks.bed.gz'\n              : \"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        }\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      {walks ? (\n        <TextField\n          className={classes.field}\n          value={haplotypes}\n          onChange={event => {\n            setHaplotypes(event.target.value)\n          }}\n          label=\"Haplotypes\"\n          slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-input' } }}\n          helperText=\"Optional. The haplotypes the track cuts for until you pick others in its menu, as PanSN names separated by commas (HG002#1, or HG002 for both); blank is every haplotype in the file\"\n          placeholder=\"HG002, HG00733\"\n          fullWidth\n        />\n      ) : null}\n      <TextField\n        className={classes.field}\n        value={trackName}\n        label=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly || submitting}\n        onClick={() => {\n          void handleSubmit()\n        }}\n      >\n        {submitting ? 'Reading graph.json\u2026' : 'Submit'}\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
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+}

package/dist/chunks/{ChooseSamplesDialog-LO7FKFSS.js → ChooseSamplesDialog-7RI573UO.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=ChooseSamplesDialog-7RI573UO.js.map

package/dist/chunks/{ChooseSamplesDialog-LO7FKFSS.js.map → ChooseSamplesDialog-7RI573UO.js.map}

@@ -3,5 +3,5 @@
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   "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport PickNamesDialog from './PickNamesDialog'\n\nimport type { GraphPaneModel } from '../model'\n\ntype SamplePicker = Pick<\n  GraphPaneModel,\n  'walkRowSampleChoices' | 'walkRowSamples' | 'setWalkRowSamples'\n>\n\n// Which samples' walks walk rows show\nconst ChooseSamplesDialog = observer(function ChooseSamplesDialog({\n  model,\n  onClose,\n}: {\n  model: SamplePicker\n  onClose: () => void\n}) {\n  const { samples } = model.walkRowSampleChoices\n  return (\n    <PickNamesDialog\n      title=\"Choose samples\"\n      label=\"Samples\"\n      testId=\"graph-choose-samples\"\n      caption={`${samples.length.toLocaleString()} samples in this cut. Their walks show in pairs, in the order picked.`}\n      options={samples}\n      initial={model.walkRowSamples ?? []}\n      confirmLabel={picked =>\n        picked.length > 0 ? 'Show these samples' : 'Show every sample'\n      }\n      onPick={picked => {\n        model.setWalkRowSamples(picked.length > 0 ? picked : undefined)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseSamplesDialog\n"],
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+  "names": ["ChooseSamplesDialog", "observer", "model", "onClose", "samples", "jsx", "PickNamesDialog_default", "picked", "ChooseSamplesDialog_default"]
 }

package/dist/chunks/{ChooseWalksDialog-JJSOVCEU.js → ChooseWalksDialog-4LDYDQH2.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=ChooseWalksDialog-4LDYDQH2.js.map

package/dist/chunks/{ChooseWalksDialog-JJSOVCEU.js.map → ChooseWalksDialog-4LDYDQH2.js.map}

@@ -3,5 +3,5 @@
   "sources": ["../../src/GraphGenomeView/components/ChooseWalksDialog.tsx"],
   "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport PickNamesDialog from './PickNamesDialog'\n\nimport type { GraphPaneModel } from '../model'\n\ntype WalkPicker = Pick<\n  GraphPaneModel,\n  'walkChoices' | 'walkLayers' | 'walkLabel' | 'liftAmongChoices'\n>\n\n// Which haplotypes to highlight, for a graph with more walks than a menu can\n// list\nconst ChooseWalksDialog = observer(function ChooseWalksDialog({\n  model,\n  onClose,\n}: {\n  model: WalkPicker\n  onClose: () => void\n}) {\n  const { walkChoices } = model\n  return (\n    <PickNamesDialog\n      title=\"Choose haplotypes\"\n      label=\"Haplotypes\"\n      testId=\"graph-choose-walks\"\n      caption={`${walkChoices.length.toLocaleString()} haplotypes in this cut. The ones picked are highlighted in this order, and the rest fades.`}\n      options={walkChoices.map(c => c.name)}\n      initial={model.walkLayers.map(l => l.walk)}\n      optionLabel={name => model.walkLabel(name)}\n      confirmLabel={picked =>\n        picked.length > 0 ? 'Highlight these' : 'Clear highlights'\n      }\n      onPick={picked => {\n        model.liftAmongChoices(picked)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseWalksDialog\n"],
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-  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
+  "names": ["ChooseWalksDialog", "observer", "model", "onClose", "walkChoices", "jsx", "PickNamesDialog_default", "c", "l", "name", "picked", "ChooseWalksDialog_default"]
 }

package/dist/chunks/{GbzBaseSyntenyAdapter-CJQVZJPA.js → GbzBaseSyntenyAdapter-W5W2JTWJ.js}

@@ -1,2 +1,2 @@
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Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-W5W2JTWJ.js.map

package/dist/chunks/{GraphGenomeView-EM7KNQHB.js → GraphGenomeView-RD2XGX6D.js}

@@ -1,4 +1,4 @@
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+//# sourceMappingURL=GraphGenomeView-RD2XGX6D.js.map

package/dist/chunks/GraphTrackSettingsDialog-R3XOY32L.js

@@ -0,0 +1,4 @@
+import{a as G,b as L}from"./chunk-4XY7HUQR.js";import{b as v,c as x,p as f}from"./chunk-X2QGBINE.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-ELC7POI6.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-J2PN6CG3.js";import{F as y,H as h,n as H}from"./chunk-WE7DQVXF.js";import{b as p,c as i,d as s}from"./chunk-DUU6T2I5.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=s(function({model:t}){let{classes:o}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?i("div",{className:o.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:n=>{t.setSubgraphContext(Number(n)),t.recut()}}),p(h,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),M=F;var I=f()({section:{marginBottom:24}});function A(a){return a.split(/[\s,]+/).filter(t=>t!=="")}var N=(a,t)=>a.join(`
+`)===t.join(`
+`);function P(a,t){let o=a.cutHaplotypes??[],[e,n]=d(o);return N(o,e)||(n(o),t()),r=>{N(r,o)||(n(r),a.setSubgraphHaplotypes(r),a.recut())}}var D=s(function({model:t}){let[o,e]=d(t.cutHaplotypes?.join(", ")??""),n=P(t,()=>{e(t.cutHaplotypes?.join(", ")??"")}),r=()=>{n(A(o))};return p(y,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:o,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:c=>{e(c.target.value)},onBlur:()=>{r()},onKeyDown:c=>{c.key==="Enter"&&r()}})}),B=s(function({model:t,names:o}){let[e,n]=d(t.cutHaplotypes??[]),r=g(e),c=g(""),[b,S]=d(!1),C=P(t,()=>{r.current=t.cutHaplotypes??[],n(r.current)});return p(H,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:o,value:e,open:b,onOpen:()=>{S(!0)},onInputChange:(u,l)=>{c.current=l},onClose:(u,l)=>{S(!1);let m=c.current.trim();l==="blur"&&m&&!r.current.includes(m)&&(r.current=[...r.current,m],n(r.current)),C(r.current)},onChange:(u,l)=>{r.current=l,n(l),b||C(l)},renderInput:u=>p(y,{...u,label:"Haplotypes",placeholder:e.length===0?"every haplotype":void 0,slotProps:{...u.slotProps,htmlInput:{...u.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),O=s(function({model:t}){let{classes:o}=I(),e=t.haplotypeNames,n=t.sourceAdapter;return n&&x(n)?i("div",{className:o.section,children:[e?p(B,{model:t,names:e}):p(D,{model:t}),i(h,{variant:"caption",component:"div",color:"text.secondary",children:[e?`Which of the graph's ${e.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),T=O;var ot=s(function({model:t,onClose:o}){return i(L,{model:t,onClose:o,children:[p(M,{model:t}),p(T,{model:t})]})});export{ot as default};
+//# sourceMappingURL=GraphTrackSettingsDialog-R3XOY32L.js.map

package/dist/chunks/{GraphTrackSettingsDialog-GTQ6Z2HA.js.map → GraphTrackSettingsDialog-R3XOY32L.js.map}

@@ -1,7 +1,7 @@
 {
   "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 sameList = (a: readonly string[], b: readonly string[]) =>\n  a.join('\\n') === b.join('\\n')\n\n// The cut's set, and the last one this field saw: an outside change (a\n// restored session, a launch) resets the draft, while the field's own apply\n// records what it set first, so it keeps its focus and draft\nfunction useCutHaplotypes(model: LinearGraphCutModel, reset: () => void) {\n  const current = model.cutHaplotypes ?? []\n  const [seen, setSeen] = useState(current)\n  if (!sameList(current, seen)) {\n    setSeen(current)\n    reset()\n  }\n  return (haplotypes: string[]) => {\n    if (!sameList(haplotypes, current)) {\n      setSeen(haplotypes)\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const setCut = useCutHaplotypes(model, () => {\n    setDraft(model.cutHaplotypes?.join(', ') ?? '')\n  })\n  const apply = () => {\n    setCut(parseHaplotypeList(draft))\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 = useCutHaplotypes(model, () => {\n    draftRef.current = model.cutHaplotypes ?? []\n    setDraft(draftRef.current)\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\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField model={model} names={names} />\n      ) : (\n        <HaplotypeListField 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"],
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-  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "jsx", "LabelledSelect", "hops", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "sameList", "a", "b", "useCutHaplotypes", "model", "reset", "current", "seen", "setSeen", "useState", "haplotypes", "HaplotypeListField", "observer", "draft", "setDraft", "setCut", "apply", "jsx", "TextField", "e", "HaplotypePickField", "names", "draftRef", "useRef", "typed", "open", "setOpen", "Autocomplete", "_", "reason", "value", "params", "SubgraphHaplotypesField", "classes", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
+  "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 sameList = (a: readonly string[], b: readonly string[]) =>\n  a.join('\\n') === b.join('\\n')\n\n// The cut's set, and the last one this field saw: an outside change (a\n// restored session, a launch) resets the draft, while the field's own apply\n// records what it set first, so it keeps its focus and draft\nfunction useCutHaplotypes(model: LinearGraphCutModel, reset: () => void) {\n  const current = model.cutHaplotypes ?? []\n  const [seen, setSeen] = useState(current)\n  if (!sameList(current, seen)) {\n    setSeen(current)\n    reset()\n  }\n  return (haplotypes: string[]) => {\n    if (!sameList(haplotypes, current)) {\n      setSeen(haplotypes)\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const setCut = useCutHaplotypes(model, () => {\n    setDraft(model.cutHaplotypes?.join(', ') ?? '')\n  })\n  const apply = () => {\n    setCut(parseHaplotypeList(draft))\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 = useCutHaplotypes(model, () => {\n    draftRef.current = model.cutHaplotypes ?? []\n    setDraft(draftRef.current)\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\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField model={model} names={names} />\n      ) : (\n        <HaplotypeListField 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 { observer } from 'mobx-react'\n\nimport SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default observer(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"],
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+  "names": ["useStyles", "makeStyles", "SUBGRAPH_CONTEXTS", "SubgraphContextSelect", "observer", "model", "classes", "adapter", "walkIndexed", "jsxs", "jsx", "LabelledSelect_default", "hops", "Typography", "SubgraphContextSelect_default", "useStyles", "makeStyles", "parseHaplotypeList", "text", "name", "sameList", "b", "useCutHaplotypes", "model", "reset", "current", "seen", "setSeen", "useState", "haplotypes", "HaplotypeListField", "observer", "draft", "setDraft", "setCut", "apply", "jsx", "TextField", "e", "HaplotypePickField", "names", "draftRef", "useRef", "typed", "open", "setOpen", "Autocomplete", "_", "reason", "value", "params", "SubgraphHaplotypesField", "classes", "adapter", "cutsByHaplotype", "jsxs", "Typography", "SubgraphHaplotypesField_default", "GraphTrackSettingsDialog_default", "observer", "model", "onClose", "jsxs", "GraphSettingsDialog_default", "jsx", "SubgraphContextSelect_default", "SubgraphHaplotypesField_default"]
 }

package/dist/chunks/HighlightColorDialog-AKPIC56I.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=HighlightColorDialog-AKPIC56I.js.map

package/dist/chunks/{HighlightColorDialog-KNJFIFLO.js.map → HighlightColorDialog-AKPIC56I.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/HighlightColorDialog.tsx"],
-  "sourcesContent": ["import { WALK_FIELDS, WALK_SCHEMES } from '@jbrowse/bandage-core/walkEncoding'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  MenuItem,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\ntype HighlightColors = Pick<\n  GraphPaneModel,\n  'drawnWalks' | 'walkLabel' | 'setWalkColor'\n>\n\nconst HighlightColorDialog = observer(function HighlightColorDialog({\n  model,\n  onClose,\n}: {\n  model: HighlightColors\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Color highlighted haplotypes\">\n      <DialogContent\n        sx={{\n          display: 'grid',\n          gridTemplateColumns: 'auto 1fr 1fr',\n          alignItems: 'center',\n          gap: 1.5,\n        }}\n      >\n        <Typography variant=\"subtitle2\">Haplotype</Typography>\n        <Typography variant=\"subtitle2\">Color by</Typography>\n        <Typography variant=\"subtitle2\">Palette</Typography>\n        {model.drawnWalks.map(({ name, encoding }) => (\n          <Row\n            key={name}\n            label={model.walkLabel(name)}\n            field={encoding.field}\n            scheme={encoding.scheme}\n            onField={field => {\n              model.setWalkColor(name, { field })\n            }}\n            onScheme={scheme => {\n              model.setWalkColor(name, { scheme })\n            }}\n          />\n        ))}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Done\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\ntype Field = (typeof WALK_FIELDS)[number]['value']\ntype Scheme = (typeof WALK_SCHEMES)[number]['value']\n\nfunction Row({\n  label,\n  field,\n  scheme,\n  onField,\n  onScheme,\n}: {\n  label: string\n  field: Field\n  scheme: Scheme\n  onField: (field: Field) => void\n  onScheme: (scheme: Scheme) => void\n}) {\n  return (\n    <>\n      <Typography variant=\"body2\">{label}</Typography>\n      <TextField\n        select\n        size=\"small\"\n        value={field}\n        slotProps={{\n          select: { SelectDisplayProps: { 'aria-label': `Color ${label} by` } },\n        }}\n        onChange={e => {\n          onField(e.target.value as Field)\n        }}\n      >\n        {WALK_FIELDS.map(f => (\n          <MenuItem key={f.value} value={f.value}>\n            {f.label}\n          </MenuItem>\n        ))}\n      </TextField>\n      <TextField\n        select\n        size=\"small\"\n        value={scheme}\n        slotProps={{\n          select: {\n            SelectDisplayProps: { 'aria-label': `Palette for ${label}` },\n          },\n        }}\n        onChange={e => {\n          onScheme(e.target.value as Scheme)\n        }}\n      >\n        {WALK_SCHEMES.filter(\n          s => s.value !== 'rainbow' || field === 'reference',\n        ).map(s => (\n          <MenuItem key={s.value} value={s.value}>\n            {s.label}\n          </MenuItem>\n        ))}\n      </TextField>\n    </>\n  )\n}\n\nexport default HighlightColorDialog\n"],
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+  "sourcesContent": ["import { WALK_FIELDS, WALK_SCHEMES } from '@jbrowse/bandage-core/walkEncoding'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  MenuItem,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\ntype HighlightColors = Pick<\n  GraphPaneModel,\n  'drawnWalks' | 'walkLabel' | 'setWalkColor'\n>\n\nconst HighlightColorDialog = observer(function HighlightColorDialog({\n  model,\n  onClose,\n}: {\n  model: HighlightColors\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Color highlighted haplotypes\">\n      <DialogContent\n        sx={{\n          display: 'grid',\n          gridTemplateColumns: 'auto 1fr 1fr',\n          alignItems: 'center',\n          gap: 1.5,\n        }}\n      >\n        <Typography variant=\"subtitle2\">Haplotype</Typography>\n        <Typography variant=\"subtitle2\">Color by</Typography>\n        <Typography variant=\"subtitle2\">Palette</Typography>\n        {model.drawnWalks.map(({ name, encoding }) => (\n          <Row\n            key={name}\n            label={model.walkLabel(name)}\n            field={encoding.field}\n            scheme={encoding.scheme}\n            onField={field => {\n              model.setWalkColor(name, { field })\n            }}\n            onScheme={scheme => {\n              model.setWalkColor(name, { scheme })\n            }}\n          />\n        ))}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Done\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\ntype Field = (typeof WALK_FIELDS)[number]['value']\ntype Scheme = (typeof WALK_SCHEMES)[number]['value']\n\nconst Row = observer(function Row({\n  label,\n  field,\n  scheme,\n  onField,\n  onScheme,\n}: {\n  label: string\n  field: Field\n  scheme: Scheme\n  onField: (field: Field) => void\n  onScheme: (scheme: Scheme) => void\n}) {\n  return (\n    <>\n      <Typography variant=\"body2\">{label}</Typography>\n      <TextField\n        select\n        size=\"small\"\n        value={field}\n        slotProps={{\n          select: { SelectDisplayProps: { 'aria-label': `Color ${label} by` } },\n        }}\n        onChange={e => {\n          onField(e.target.value as Field)\n        }}\n      >\n        {WALK_FIELDS.map(f => (\n          <MenuItem key={f.value} value={f.value}>\n            {f.label}\n          </MenuItem>\n        ))}\n      </TextField>\n      <TextField\n        select\n        size=\"small\"\n        value={scheme}\n        slotProps={{\n          select: {\n            SelectDisplayProps: { 'aria-label': `Palette for ${label}` },\n          },\n        }}\n        onChange={e => {\n          onScheme(e.target.value as Scheme)\n        }}\n      >\n        {WALK_SCHEMES.filter(\n          s => s.value !== 'rainbow' || field === 'reference',\n        ).map(s => (\n          <MenuItem key={s.value} value={s.value}>\n            {s.label}\n          </MenuItem>\n        ))}\n      </TextField>\n    </>\n  )\n})\n\nexport default HighlightColorDialog\n"],
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   "names": ["HighlightColorDialog", "observer", "model", "onClose", "jsxs", "Dialog", "DialogContent", "jsx", "Typography", "name", "encoding", "Row", "field", "scheme", "DialogActions", "Button", "label", "onField", "onScheme", "Fragment", "TextField", "WALK_FIELDS", "f", "MenuItem", "WALK_SCHEMES", "s", "HighlightColorDialog_default"]
 }

package/dist/chunks/{LinearGraphDisplay-APDIIF7F.js → LinearGraphDisplay-RRAXTQFC.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=LinearGraphDisplay-APDIIF7F.js.map
+import{a,b as i}from"./chunk-Y7MQVQAS.js";import"./chunk-4XY7HUQR.js";import"./chunk-DIGIM3XY.js";import"./chunk-WE7XHNAH.js";import"./chunk-X2QGBINE.js";import"./chunk-WO644UAC.js";import"./chunk-4DQWDJG7.js";import"./chunk-UC2NHZ7E.js";import"./chunk-OPWSPSAE.js";import"./chunk-W5HHWDGZ.js";import"./chunk-E23AOQPE.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as o,d as t}from"./chunk-DUU6T2I5.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
+//# sourceMappingURL=LinearGraphDisplay-RRAXTQFC.js.map

package/dist/chunks/LinearGraphDisplay-RRAXTQFC.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["jbrowse-host:@jbrowse/display-kit/DisplayChrome", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/DisplayChrome\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayChrome\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "import DisplayChrome from '@jbrowse/display-kit/DisplayChrome'\nimport { observer } from 'mobx-react'\n\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\nimport { createGraphRenderer } from '../../GraphGenomeView/renderer/GraphRenderer'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <DisplayChrome\n      model={model}\n      factory={createGraphRenderer}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      {handle => <GraphCanvas model={model} handle={handle} />}\n    </DisplayChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
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+  "names": ["host", "DisplayChrome_default", "host", "LinearGraphDisplay", "observer", "model", "jsx", "DisplayChrome_default", "createGraphRenderer", "handle", "GraphCanvas_default", "LinearGraphDisplay_default"]
+}

package/dist/chunks/{MinigraphBubbleAdapter-QEC37MYN.js → MinigraphBubbleAdapter-NWINKWTS.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-W5HHWDGZ.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-QEC37MYN.js.map
+import{a as f,d as c,f as d}from"./chunk-W5HHWDGZ.js";import{a as g}from"./chunk-V55TK2NP.js";import{E as p,F as u,b,z as m}from"./chunk-ZT2SESHC.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as i,o as l}from"./chunk-TC265JAP.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-NWINKWTS.js.map

package/dist/chunks/{RgfaTabixAdapter-ZGXDNU43.js → RgfaTabixAdapter-N44KY4YC.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=RgfaTabixAdapter-ZGXDNU43.js.map
+import{a as F}from"./chunk-YVYWV36O.js";import"./chunk-ZA5GPTUM.js";import{a as N}from"./chunk-V55TK2NP.js";import"./chunk-YBLNN5FU.js";import"./chunk-U6SNNNFV.js";import"./chunk-ELC7POI6.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-ZT2SESHC.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as l,o as m}from"./chunk-TC265JAP.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
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package/dist/chunks/{TrackWarningsDialog-4YDIV2FN.js → TrackWarningsDialog-23WL6FPV.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=TrackWarningsDialog-4YDIV2FN.js.map
+import{H as i,h as o,m as a}from"./chunk-WE7DQVXF.js";import{c as r,d as e}from"./chunk-DUU6T2I5.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
+//# sourceMappingURL=TrackWarningsDialog-23WL6FPV.js.map

package/dist/chunks/{TrackWarningsDialog-4YDIV2FN.js.map → TrackWarningsDialog-23WL6FPV.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.18_@emotion+react@11.14.0_@types+react@19.3.0_react@19_0b9c1c4d2b16eef60d202e26c552208a/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.19_@emotion+react@11.14.0_@types+react@19.3.0_react@19_eb34fd01d29d05a1c3ac8167d41484d7/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
   "sourcesContent": ["import { jsxs as _jsxs } from \"react/jsx-runtime\";\nimport { InfoDialog } from '@jbrowse/core/ui';\nimport { Alert, Typography } from '@mui/material';\nimport { observer } from 'mobx-react';\n/**\n * The render-warnings report both comparative views open, over the rows\n * `collectTrackWarnings` builds for them. Reads them off the view rather than\n * taking a copy, so a refetch that raises or clears a warning while the dialog\n * is open shows in it.\n *\n * Grouped by track, with the track name leading each row: a stacked view's\n * levels raise the same swapped-assemblies warning verbatim, and so does every\n * overlaid track that hits it, so an ungrouped list repeated one sentence N\n * times without ever naming the file to go fix.\n *\n * Keyed by position \u2014 the message is not an identity, and neither is the track\n * name once one track raises two warnings.\n */\nconst TrackWarningsDialog = observer(function TrackWarningsDialog({ model, title, children, handleClose, }) {\n    return (_jsxs(InfoDialog, { open: true, title: title, onClose: () => {\n            handleClose();\n        }, children: [children, model.trackWarnings.flatMap(({ name, warnings }, i) => warnings.map((w, j) => (_jsxs(Alert\n            // eslint-disable-next-line @eslint-react/no-array-index-key -- see above\n            , { severity: \"warning\", style: { marginBottom: 8 }, children: [_jsxs(Typography, { variant: \"subtitle2\", children: [name, \": \", w.message] }), w.effect] }, `${i}_${j}`))))] }));\n});\nexport default TrackWarningsDialog;\n"],
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   "names": ["TrackWarningsDialog", "observer", "model", "title", "children", "handleClose", "jsxs", "InfoDialog", "name", "warnings", "i", "w", "j", "Alert", "Typography", "TrackWarningsDialog_default"]

package/dist/chunks/{WalkFormsAdapter-QYFYWQJD.js → WalkFormsAdapter-VDL5XWSU.js}

@@ -1,2 +1,2 @@
-import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-4LAVXP7J.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-PX4IRCTO.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-CL4PYWKC.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-QYFYWQJD.js.map
+import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-YTTNQYSM.js";import{a as k}from"./chunk-V55TK2NP.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-ZT2SESHC.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-CL4PYWKC.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as m,o as u}from"./chunk-TC265JAP.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-VDL5XWSU.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-F4XTB7W4.js → WalkTabixSyntenyAdapter-RGJWOHJG.js}

@@ -1,2 +1,2 @@
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o=new Map,e=s=>{let n=P(r,s),i=o.get(n);return i===void 0&&(i="N".repeat(n),o.set(n,i)),i},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=R(s),t.set(s,n)),n};return(s,n)=>H({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var _=100;function I(r,o,e){let t=r.at(-1);e>0&&(t?.[0]===o?t[1]+=e:r.push([o,e]))}function ae(r){let o=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+o(s)}),a};return(t,a)=>{let s=R(a),n=R(t),[i,c]=L(n,s,o),[h,d]=L(n.map(y=>y^1).reverse(),s,o),m=d>c,p=m?h:i,b=Math.max(c,d);if(b<_)return[];let f=e(s),g=e(n),u=y=>m?n.length-1-p[y][0]:p[y][0],k=[];p.forEach(([,y],N)=>{if(N>0){let[M,l]=[u(N-1),u(N)].sort((w,C)=>w-C);I(k,"I",g[l]-g[M+1]),I(k,"D",f[y]-f[p[N-1][1]+1])}I(k,"=",o(s[y]))});let[S,W]=[u(0),u(p.length-1)].sort((y,N)=>y-N);return[{queryStart:g[S],queryEnd:g[W+1],targetStart:f[p[0][1]],targetEnd:f[p.at(-1)[1]+1],strand:m?"-":"+",edits:k,sharedBases:b}]}}function ce(r){let o=new Map,e=new Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=ce(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,h]of e(t)){let d=s.get(c);d===h?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var pe=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:h}=t(a,s);return i===void 0||Math.min(c,h)<pe?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function j({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=le(r.edits);return Y({target:{name:o.name,assemblyName:t,refName:a,start:o.hapStart+r.targetStart,end:o.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:A(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:q(n),matches:n.reduce((i,[c,h])=>i+(c==="="?h:0),0),columns:n.reduce((i,[,c])=>i+c,0)})}function ie(r,o,e,t,a){let s=a==="leave",n=i=>i.kind==="elsewhere"&&(s?i.chunk.start>=r.refStart:i.chunk.start<r.refStart);for(let i of e){let{name:c,fragStart:h,hapStart:d,ids:m,rev:p,before:b,after:f}=i;if(c===r.name&&h===r.fragStart){let g=d;for(let u=0;u<m.length;u++){let k=t.get(m[u]),S=k===void 0?0:k.end-k.start;if(k?.rank===0&&k.refName===o&&(s?k.end===r.refStart:k.start===r.refEnd)){let W=n(f)!==n(b)?n(f):u>0!=u<m.length-1?u>0:s!==(p[u]===1);return{skip:r,at:W?g+S:g,strand:W===s?"+":"-"}}g+=S}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r,i=`${a.name}:${a.fragStart}:${a.piece}:skip`;return new K({uniqueId:i,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,type:"deletion",strand:n==="-"?-1:1,syntenyId:i,spansWindow:!0,mate:{refName:A(a.name),start:s,end:s,assemblyName:t}})}var T=({name:r})=>D(r)??r,$=class extends V{constructor(){super(...arguments);this.walks=new ee(X(this,["walksLocation"],["walksIndex"]),this);this.refNames=new z(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=F(this,a),n=E(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&O(i)!==s).map(i=>({name:B(n,i),label:i,group:O(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=U(a,e);return v(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let h=new Set(c.map(d=>d.skip));n=n.filter(d=>!h.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=m=>a==="leave"?m.refStart-1:m.refEnd,h=new Map;for(let m of t){let p=c(m),b=Math.floor(p/i),f=h.get(b);f?(f.group.push(m),f.start=Math.min(f.start,p),f.end=Math.max(f.end,p+1)):h.set(b,{group:[m],start:p,end:p+1})}return(await Promise.all([...h.values()].map(async({group:m,start:p,end:b})=>{let f=new Set(m.map(u=>u.name)),g=u=>f.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:p,end:b},{...this.walks.budgets(),signal:n,keep:g,expand:g,context:0,contained:!0,links:!1});return m.map(S=>ie(S,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(m=>m!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(l=>F(this,l)):void 0,n=F(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(l=>x(n,l)||x(l,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:h}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${h.toLocaleString()}`,{graph:m,fragments:p,skips:b}=await this.laneWalks(e,t,i,a,d),f=({name:l})=>i===void 0?0:i.findIndex(w=>x(l,w)),g=new Set(p.map(T)),u=await v(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(l=>f(l)>=0&&!g.has(T(l))&&l.refStart<=c&&l.refEnd>=h),a)),k=re(m.nodes),S=E(this),W=l=>B(S,T(l)),y=p.filter(l=>l.name===e),N=p.filter(l=>l.name!==e&&f(l)>=0).map(l=>({rank:f(l),features:y.flatMap(w=>k(l,w).map(C=>j({chain:C,target:w,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:W(l)})))})),M=u.map(l=>({rank:f(l.skip),features:[oe({crossing:l,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:W(l.skip)})]}));return[...N,...M].sort((l,w)=>l.rank-w.rank).flatMap(l=>l.features)}async pairFeatures(e,t,a,s){let n=a.map(m=>({pair:m,featurePrefix:F(this,m.queryAssemblyName),matePrefix:F(this,m.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(m=>[m.featurePrefix,m.matePrefix]),s,J(a)),h=se(i.nodes),d=m=>c.filter(p=>x(p.name,m));return n.flatMap(({pair:m,featurePrefix:p,matePrefix:b})=>d(p).flatMap(f=>d(b).flatMap(g=>h(g,f).map(u=>j({chain:u,target:f,query:g,assemblyName:m.queryAssemblyName,refName:A(f.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return G(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=Z(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{$ as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-F4XTB7W4.js.map
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Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=ce(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,h]of e(t)){let d=s.get(c);d===h?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var pe=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:h}=t(a,s);return i===void 0||Math.min(c,h)<pe?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function j({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=le(r.edits);return 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K({uniqueId:i,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,type:"deletion",strand:n==="-"?-1:1,syntenyId:i,spansWindow:!0,mate:{refName:A(a.name),start:s,end:s,assemblyName:t}})}var T=({name:r})=>D(r)??r,$=class extends V{constructor(){super(...arguments);this.walks=new ee(X(this,["walksLocation"],["walksIndex"]),this);this.refNames=new z(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=F(this,a),n=E(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&O(i)!==s).map(i=>({name:B(n,i),label:i,group:O(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=U(a,e);return v(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let h=new Set(c.map(d=>d.skip));n=n.filter(d=>!h.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=m=>a==="leave"?m.refStart-1:m.refEnd,h=new Map;for(let m of t){let p=c(m),b=Math.floor(p/i),f=h.get(b);f?(f.group.push(m),f.start=Math.min(f.start,p),f.end=Math.max(f.end,p+1)):h.set(b,{group:[m],start:p,end:p+1})}return(await Promise.all([...h.values()].map(async({group:m,start:p,end:b})=>{let f=new Set(m.map(u=>u.name)),g=u=>f.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:p,end:b},{...this.walks.budgets(),signal:n,keep:g,expand:g,context:0,contained:!0,links:!1});return m.map(S=>ie(S,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(m=>m!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(l=>F(this,l)):void 0,n=F(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(l=>x(n,l)||x(l,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:h}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${h.toLocaleString()}`,{graph:m,fragments:p,skips:b}=await this.laneWalks(e,t,i,a,d),f=({name:l})=>i===void 0?0:i.findIndex(w=>x(l,w)),g=new Set(p.map(T)),u=await v(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(l=>f(l)>=0&&!g.has(T(l))&&l.refStart<=c&&l.refEnd>=h),a)),k=re(m.nodes),S=E(this),W=l=>B(S,T(l)),y=p.filter(l=>l.name===e),N=p.filter(l=>l.name!==e&&f(l)>=0).map(l=>({rank:f(l),features:y.flatMap(w=>k(l,w).map(C=>j({chain:C,target:w,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:W(l)})))})),M=u.map(l=>({rank:f(l.skip),features:[oe({crossing:l,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:W(l.skip)})]}));return[...N,...M].sort((l,w)=>l.rank-w.rank).flatMap(l=>l.features)}async pairFeatures(e,t,a,s){let n=a.map(m=>({pair:m,featurePrefix:F(this,m.queryAssemblyName),matePrefix:F(this,m.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(m=>[m.featurePrefix,m.matePrefix]),s,J(a)),h=se(i.nodes),d=m=>c.filter(p=>x(p.name,m));return n.flatMap(({pair:m,featurePrefix:p,matePrefix:b})=>d(p).flatMap(f=>d(b).flatMap(g=>h(g,f).map(u=>j({chain:u,target:f,query:g,assemblyName:m.queryAssemblyName,refName:A(f.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return G(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=Z(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{$ as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-RGJWOHJG.js.map

package/dist/chunks/chunk-4XY7HUQR.js

@@ -0,0 +1,2 @@
+import{i as M,l as W,p as F}from"./chunk-X2QGBINE.js";import{b as O,h as B}from"./chunk-UC2NHZ7E.js";import{K as f,Q as A,X as _}from"./chunk-OPWSPSAE.js";import{f as R}from"./chunk-J2PN6CG3.js";import{D as x,E,H as S,d as C,o as T,q as I,r as w,s as L,t as N,w as D,y as G,z as P}from"./chunk-WE7DQVXF.js";import{b as t,c as r,d as s}from"./chunk-DUU6T2I5.js";var k=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var U=s(function({label:n,value:e,options:o,testId:p,size:h,sx:a,disabled:m,title:u,shown:b,onChange:H}){let y=R();return r(L,{size:h,sx:a,disabled:m,title:u,children:[t(D,{id:y,shrink:!0,children:n}),t(x,{labelId:y,value:e,label:n,notched:!0,displayEmpty:!0,"data-testid":p,renderValue:i=>b??o.find(Y=>Y.value===i)?.label??i,onChange:i=>{H(i.target.value)},children:o.map(i=>t(P,{value:i.value,disabled:i.disabled,title:i.disabled?void 0:i.description,children:t(G,{primary:i.label,secondary:i.disabled?i.description:void 0})},i.value))})]})});var g=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}}),l=s(function({warn:n=!1,children:e}){return t(S,{variant:"caption",component:"div",color:n?"warning.main":"text.secondary",children:e})}),v=s(function({title:n,children:e}){let{classes:o}=g();return r("section",{className:o.group,children:[t(S,{variant:"subtitle1",className:o.heading,children:n}),e]})}),Q=s(function({label:n,checked:e,onChange:o,children:p}){let{classes:h}=g();return r("div",{className:h.section,children:[t(N,{control:t(E,{checked:e,onChange:a=>{o(a.target.checked)}}),label:n}),p]})}),d=s(function({children:n,...e}){let{classes:o}=g();return r("div",{className:o.section,children:[t(U,{sx:{minWidth:200},...e}),n]})}),$=[5e3,2e4,5e4,1e5];function q(c){return[...new Set([...$,c])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}var z=s(function({label:n,choices:e,stored:o,auto:p,testId:h,onChange:a,children:m}){return e.length>0?t(d,{label:n,value:e.some(u=>u.trackId===o)?o:"",options:[{value:"",label:`Automatic (${p?.name??"none"})`},...e.map(({trackId:u,name:b})=>({value:u,label:b}))],testId:h,onChange:a,children:m}):null}),K=s(function(n){let{model:e,onClose:o,children:p}=n,{classes:h}=g();return r(C,{open:!0,onClose:o,title:"Graph settings",children:[r(w,{children:[r(v,{title:"Subgraph",children:[p,t(d,{label:"Node limit",value:String(e.maxGraphNodes),options:q(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(l,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),r(v,{title:"Drawing",children:[e.anchorPaths.length>1?t(d,{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(l,{children:"The path the anchored layouts place x along"})}):null,t(d,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(l,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),t(d,{label:"Link width",value:e.linkWidth,options:_,testId:"graph-link-width-select",onChange:a=>{e.setLinkWidth(a)},children:t(l,{children:"Walks as width, so a common route reads heavy and a private one thin."})}),r(Q,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(l,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(l,{warn:!0,children:e.pathCount>f?`Off: ${e.pathCount.toLocaleString()} paths is past the ${f} this can tell apart`:"Off: this graph states no paths"}):null]}),t(z,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:W(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(l,{children:"Where genes on the backbone come from"})}),t(z,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:M(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(l,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),r(v,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:h.section,children:t(l,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(d,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(l,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(d,{label:"Layout quality",value:String(e.layoutQuality),options:k.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(l,{children:"The engine's iteration budget; higher is slower"})}),t(d,{label:"Bubble spread",value:e.bubbleSpread,options:B,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(l,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(Q,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(l,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:o,children:"Close"})})]})}),be=K;export{U as a,be as b};
+//# sourceMappingURL=chunk-4XY7HUQR.js.map

package/dist/chunks/chunk-4XY7HUQR.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default observer(function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n})\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { EDGE_WIDTHS } from '@jbrowse/bandage-core/edgeWidths'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\n  },\n})\n\nconst Caption = observer(function Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n})\n\nconst Group = observer(function Group({\n  title,\n  children,\n}: {\n  title: string\n  children: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\n})\n\nconst SettingSwitch = observer(function SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n})\n\n// one dropdown setting, at the dialog's width, and its caption\nconst SettingSelect = observer(function SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n})\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nconst TrackPickSetting = observer(function TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n})\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            >\n              <Caption>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          >\n            <Caption>\n              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Link width\"\n            value={model.linkWidth}\n            options={EDGE_WIDTHS}\n            testId=\"graph-link-width-select\"\n            onChange={links => {\n              model.setLinkWidth(links)\n            }}\n          >\n            <Caption>\n              Walks as width, so a common route reads heavy and a private one\n              thin.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\n            </Caption>\n            {model.drawPaths && !model.effectiveDrawPaths ? (\n              <Caption warn>\n                {model.pathCount > MAX_PATH_COLORS\n                  ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                  : 'Off: this graph states no paths'}\n              </Caption>\n            ) : null}\n          </SettingSwitch>\n\n          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? (\n            <div className={classes.section}>\n              <Caption warn>\n                No effect on the current layout until Layout is Force-directed\n              </Caption>\n            </div>\n          ) : null}\n\n          <SettingSelect\n            label=\"Engine\"\n            value={model.layoutEngine}\n            options={LAYOUT_ENGINES}\n            testId=\"graph-layout-engine-select\"\n            onChange={engine => {\n              model.setLayoutEngine(engine)\n            }}\n          >\n            <Caption>\n              Stress keeps the reference straight, so a zoom keeps the picture;\n              FMMM lets the whole graph settle.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Layout quality\"\n            value={String(model.layoutQuality)}\n            options={LAYOUT_QUALITIES.map(q => ({\n              value: String(q.value),\n              label: q.label,\n            }))}\n            testId=\"graph-layout-quality-select\"\n            onChange={quality => {\n              model.setLayoutQuality(Number(quality))\n            }}\n          >\n            <Caption>\n              The engine&apos;s iteration budget; higher is slower\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n            }}\n          >\n            <Caption>How far the layout opens a bubble</Caption>\n          </SettingSelect>\n\n          {model.layoutEngine === 'stress' ? null : (\n            <SettingSwitch\n              label=\"Linear layout\"\n              checked={model.linearLayout}\n              onChange={linear => {\n                model.setLinearLayout(linear)\n              }}\n            >\n              <Caption>Keeps a chain of nodes on one line where it can</Caption>\n            </SettingSwitch>\n          )}\n        </Group>\n      </DialogContent>\n\n      <DialogActions>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GraphSettingsDialog\n"],
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+  "names": ["LAYOUT_QUALITIES", "LabelledSelect_default", "observer", "label", "value", "options", "testId", "size", "sx", "disabled", "title", "shown", "onChange", "labelId", "useId", "jsxs", "FormControl", "jsx", "InputLabel", "Select", "picked", "o", "e", "MenuItem", "ListItemText", "useStyles", "makeStyles", "Caption", "observer", "warn", "children", "jsx", "Typography", "Group", "title", "classes", "jsxs", "SettingSwitch", "label", "checked", "onChange", "FormControlLabel", "Switch", "e", "SettingSelect", "props", "LabelledSelect_default", "NODE_LIMITS", "nodeLimitOptions", "current", "a", "b", "limit", "TrackPickSetting", "choices", "stored", "auto", "testId", "t", "trackId", "name", "GraphSettingsDialog", "model", "onClose", "Dialog", "DialogContent", "NODE_WIDTHS", "width", "EDGE_WIDTHS", "links", "draw", "MAX_PATH_COLORS", "pickGeneTrack", "pickRepeatTrack", "LAYOUT_ENGINES", "engine", "LAYOUT_QUALITIES", "q", "quality", "BUBBLE_SPREADS", "spread", "linear", "DialogActions", "Button", "GraphSettingsDialog_default"]
+}

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

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=chunk-6OZGIMZC.js.map

package/dist/chunks/chunk-6OZGIMZC.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/PickNamesDialog.tsx"],
+  "sourcesContent": ["import { useState } from 'react'\nimport type { ReactNode } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Autocomplete,\n  Button,\n  Checkbox,\n  DialogActions,\n  DialogContent,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\n// A set of names picked by search, in the order picked, committed on confirm\nexport default observer(function PickNamesDialog({\n  title,\n  label,\n  caption,\n  testId,\n  options,\n  initial,\n  optionLabel = name => name,\n  confirmLabel,\n  onPick,\n  onClose,\n}: {\n  title: string\n  label: string\n  caption: ReactNode\n  testId: string\n  options: string[]\n  initial: string[]\n  optionLabel?: (name: string) => string\n  confirmLabel: (picked: string[]) => string\n  onPick: (picked: string[]) => void\n  onClose: () => void\n}) {\n  const [picked, setPicked] = useState(() =>\n    initial.filter(name => options.includes(name)),\n  )\n  return (\n    <Dialog open onClose={onClose} title={title}>\n      <DialogContent>\n        <Autocomplete\n          multiple\n          disableCloseOnSelect\n          data-testid={testId}\n          options={options}\n          getOptionLabel={optionLabel}\n          value={picked}\n          onChange={(_, value) => {\n            setPicked(value)\n          }}\n          renderOption={({ key, ...props }, name, { selected }) => (\n            <li key={key} {...props}>\n              <Checkbox size=\"small\" checked={selected} />\n              {optionLabel(name)}\n            </li>\n          )}\n          renderInput={params => (\n            <TextField\n              {...params}\n              autoFocus\n              label={label}\n              placeholder=\"type to search\"\n            />\n          )}\n        />\n        <Typography variant=\"caption\" color=\"text.secondary\">\n          {caption}\n        </Typography>\n      </DialogContent>\n      <DialogActions>\n        <Button onClick={onClose}>Cancel</Button>\n        <Button\n          variant=\"contained\"\n          onClick={() => {\n            onPick(picked)\n            onClose()\n          }}\n        >\n          {confirmLabel(picked)}\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n"],
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+  "names": ["PickNamesDialog_default", "observer", "title", "label", "caption", "testId", "options", "initial", "optionLabel", "name", "confirmLabel", "onPick", "onClose", "picked", "setPicked", "useState", "jsxs", "Dialog", "DialogContent", "jsx", "Autocomplete", "_", "value", "key", "props", "selected", "Checkbox", "params", "TextField", "Typography", "DialogActions", "Button"]
+}