jbrowse-plugin-graphgenomeviewer 6.5.0 → 6.7.0

package/README.md

@@ -73,9 +73,10 @@ Needs JBrowse 5.0.0-beta.11 or later.
 ```
 
 - **File → Open track** opens an rGFA index (`.segs.bed.gz` from
-  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`.
-  It finds the links and indexes beside the url, which a presigned url's
-  signature doesn't cover; spell out each location in a config instead
+  [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix)) or a gbz-base database
+  (`.gbz.db`) as a `GraphTrack`. It finds the links and indexes beside the url,
+  which a presigned url's signature doesn't cover; spell out each location in a
+  config instead
 - A hand-written track needs only the adapter:
 
 ```json

package/dist/chunks/AddTrackWorkflow-YGKG57NL.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-YGKG57NL.js.map

package/dist/chunks/AddTrackWorkflow-YGKG57NL.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } 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} from './buildTrackConfig'\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  '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 [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\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          assembly: model.assembly,\n          sample,\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            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 ? 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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      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"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}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
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+}

package/dist/chunks/ChooseSamplesDialog-GWMJ7B5D.js

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+//# sourceMappingURL=ChooseSamplesDialog-GWMJ7B5D.js.map

package/dist/chunks/ChooseSamplesDialog-GWMJ7B5D.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/ChooseSamplesDialog.tsx"],
+  "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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+}

package/dist/chunks/ChooseWalksDialog-6HVVZMFD.js

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+//# sourceMappingURL=ChooseWalksDialog-6HVVZMFD.js.map

package/dist/chunks/ChooseWalksDialog-6HVVZMFD.js.map

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+{
+  "version": 3,
+  "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' | 'liftWalks'\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.liftWalks(picked)\n      }}\n      onClose={onClose}\n    />\n  )\n})\n\nexport default ChooseWalksDialog\n"],
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+}