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194
packages/core/BaseFeatureWidget/SequenceFeatureDetails/dialogs/AdvancedSequenceDialog.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| import React, { Suspense, useRef, useState } from 'react' | ||
| import { | ||
| Button, | ||
| DialogContent, | ||
| DialogActions, | ||
| FormControl, | ||
| MenuItem, | ||
| Select, | ||
| Typography, | ||
| Checkbox, | ||
| FormControlLabel, | ||
| } from '@mui/material' | ||
| import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui' | ||
| import { makeStyles } from 'tss-react/mui' | ||
| import { observer } from 'mobx-react' | ||
|
|
||
| // locals | ||
| import { useFeatureSequence } from '../hooks' | ||
| import { SimpleFeatureSerialized } from '../../../util' | ||
| import { BaseFeatureWidgetModel } from '../../stateModelFactory' | ||
| import AdvancedSequencePanel from './AdvancedSequencePanel' | ||
|
|
||
| const useStyles = makeStyles()({ | ||
| dialogContent: { | ||
| width: '80em', | ||
| }, | ||
| formControl: { | ||
| margin: 0, | ||
| marginLeft: 4, | ||
| }, | ||
| }) | ||
|
|
||
| const AdvancedSequenceDialog = observer(function ({ | ||
| handleClose, | ||
| model, | ||
| feature, | ||
| }: { | ||
| handleClose: () => void | ||
| feature: SimpleFeatureSerialized | ||
| model: BaseFeatureWidgetModel | ||
| }) { | ||
| const { sequenceFeatureDetails } = model | ||
| const { intronBp, upDownBp, showCoordinates } = sequenceFeatureDetails | ||
| const { classes } = useStyles() | ||
| const seqPanelRef = useRef<HTMLDivElement>(null) | ||
|
|
||
| const [force, setForce] = useState(false) | ||
| const hasCDS = feature.subfeatures?.some(sub => sub.type === 'CDS') | ||
| const hasExon = feature.subfeatures?.some(sub => sub.type === 'exon') | ||
| const hasExonOrCDS = hasExon || hasCDS | ||
| const { sequence, error } = useFeatureSequence( | ||
| model, | ||
| feature, | ||
| upDownBp, | ||
| force, | ||
| ) | ||
|
|
||
| const [mode, setMode] = useState( | ||
| hasCDS ? 'cds' : hasExon ? 'cdna' : 'genomic', | ||
| ) | ||
| return ( | ||
| <Dialog | ||
| maxWidth="xl" | ||
| open | ||
| onClose={() => handleClose()} | ||
| title="Advanced sequence view dialog" | ||
| > | ||
| <DialogContent className={classes.dialogContent}> | ||
| <div> | ||
| <FormControlLabel | ||
| label="Show coordinates" | ||
| control={ | ||
| <Checkbox | ||
| checked={sequenceFeatureDetails.showCoordinates} | ||
| onChange={() => | ||
| sequenceFeatureDetails.setShowCoordinates( | ||
| !sequenceFeatureDetails.showCoordinates, | ||
| ) | ||
| } | ||
| /> | ||
| } | ||
| /> | ||
| <FormControl className={classes.formControl}> | ||
| <Select | ||
| size="small" | ||
| value={mode} | ||
| onChange={event => setMode(event.target.value)} | ||
| > | ||
| {Object.entries({ | ||
| ...(hasCDS | ||
| ? { | ||
| cds: 'CDS', | ||
| } | ||
| : {}), | ||
| ...(hasCDS | ||
| ? { | ||
| protein: 'Protein', | ||
| } | ||
| : {}), | ||
| ...(hasExonOrCDS | ||
| ? { | ||
| cdna: 'cDNA', | ||
| } | ||
| : {}), | ||
| ...(hasExonOrCDS | ||
| ? { | ||
| gene: `Genomic w/ full introns`, | ||
| } | ||
| : {}), | ||
| ...(hasExonOrCDS | ||
| ? { | ||
| gene_updownstream: `Genomic w/ full introns +/- ${upDownBp}bp up+down stream`, | ||
| } | ||
| : {}), | ||
| ...(hasExonOrCDS | ||
| ? { | ||
| gene_collapsed_intron: `Genomic w/ ${intronBp}bp intron`, | ||
| } | ||
| : {}), | ||
| ...(hasExonOrCDS | ||
| ? { | ||
| gene_updownstream_collapsed_intron: `Genomic w/ ${intronBp}bp intron +/- ${upDownBp}bp up+down stream `, | ||
| } | ||
| : {}), | ||
|
|
||
| ...(!hasExonOrCDS | ||
| ? { | ||
| genomic: 'Genomic', | ||
| } | ||
| : {}), | ||
| ...(!hasExonOrCDS | ||
| ? { | ||
| genomic_sequence_updownstream: `Genomic +/- ${upDownBp}bp up+down stream`, | ||
| } | ||
| : {}), | ||
| }).map(([key, val]) => ( | ||
| <MenuItem key={key} value={key}> | ||
| {val} | ||
| </MenuItem> | ||
| ))} | ||
| </Select> | ||
| </FormControl> | ||
| </div> | ||
|
|
||
| <div> | ||
| {feature.type === 'gene' ? ( | ||
| <Typography> | ||
| Note: inspect subfeature sequences for protein/CDS computations | ||
| </Typography> | ||
| ) : null} | ||
| {error ? ( | ||
| <ErrorMessage error={error} /> | ||
| ) : !sequence ? ( | ||
| <LoadingEllipses /> | ||
| ) : sequence ? ( | ||
| 'error' in sequence ? ( | ||
| <> | ||
| <Typography color="error">{sequence.error}</Typography> | ||
| <Button | ||
| variant="contained" | ||
| color="inherit" | ||
| onClick={() => setForce(true)} | ||
| > | ||
| Force load | ||
| </Button> | ||
| </> | ||
| ) : ( | ||
| <Suspense fallback={<LoadingEllipses />}> | ||
| <AdvancedSequencePanel | ||
| ref={seqPanelRef} | ||
| showCoords={showCoordinates} | ||
| feature={feature} | ||
| mode={mode} | ||
| sequence={sequence} | ||
| model={sequenceFeatureDetails} | ||
| /> | ||
| </Suspense> | ||
| ) | ||
| ) : ( | ||
| <Typography>No sequence found</Typography> | ||
| )} | ||
| </div> | ||
| </DialogContent> | ||
|
|
||
| <DialogActions> | ||
| <Button onClick={() => handleClose()} variant="contained"> | ||
| Close | ||
| </Button> | ||
| </DialogActions> | ||
| </Dialog> | ||
| ) | ||
| }) | ||
|
|
||
| export default AdvancedSequenceDialog |
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