jbrowse-plugin-graphgenomeviewer 8.7.1 → 8.7.2

package/dist/chunks/AddTrackWorkflow-FANMD3WB.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-FANMD3WB.js.map

package/dist/chunks/{AddTrackWorkflow-IOPTETLH.js.map → AddTrackWorkflow-FANMD3WB.js.map}

@@ -1,7 +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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+  "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  'WalkTabixSyntenyAdapter',\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 === 'WalkTabixSyntenyAdapter'\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. 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 }

package/dist/chunks/{GraphGenomeView-M4EGRLX4.js → GraphGenomeView-HCN57HV4.js}

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 S	1	ACGT
 S	2	GGCC
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@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
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e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?Rt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>Rt(He(t,me(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(me(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return 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t&&n?Ao(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowList(){let t=this.walkRowBars;return t?[t.reference,...t.rows]:[]},get walkRowRibbons(){let t=this.walkRowGroups?.sections??[];return e.walkRibbons&&e.rowVisitsNeeded&&this.walkRowBars?Rn(this.walkRowList).filter(({row:n})=>jt(t,n)===jt(t,n+1)):void 0},get sharedBlocks(){return e.layerSet.has("walkBlocks")&&e.rowVisitsNeeded&&this.walkRowBars?xn(this.walkRowList):void 0},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ie(e.graph,n,t):[]},get bubbleHalos(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:ln(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return at(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Xe(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return 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