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feat(web): add sequence sorting prototype
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89 changes: 89 additions & 0 deletions
89
packages_rs/nextclade-web/src/components/Autodetect/AutodetectPage.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| import React from 'react' | ||
| import { Col as ColBase, Row as RowBase } from 'reactstrap' | ||
| import { useRecoilValue } from 'recoil' | ||
| import { TableSlimWithBorders } from 'src/components/Common/TableSlim' | ||
| import { Layout } from 'src/components/Layout/Layout' | ||
| import { useTranslationSafe } from 'src/helpers/useTranslationSafe' | ||
| import { autodetectResultsAtom } from 'src/state/autodetect.state' | ||
| import styled from 'styled-components' | ||
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| const Container = styled.div` | ||
| margin-top: 1rem; | ||
| height: 100%; | ||
| overflow: hidden; | ||
| ` | ||
|
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| const Row = styled(RowBase)` | ||
| overflow: hidden; | ||
| height: 100%; | ||
| ` | ||
|
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| const Col = styled(ColBase)` | ||
| overflow: hidden; | ||
| height: 100%; | ||
| ` | ||
|
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| const Table = styled(TableSlimWithBorders)` | ||
| padding-top: 50px; | ||
| & thead { | ||
| height: 51px; | ||
| position: sticky; | ||
| top: -2px; | ||
| background-color: ${(props) => props.theme.gray700}; | ||
| color: ${(props) => props.theme.gray100}; | ||
| } | ||
| & thead th { | ||
| margin: auto; | ||
| text-align: center; | ||
| vertical-align: middle; | ||
| } | ||
| ` | ||
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| const TableWrapper = styled.div` | ||
| height: 100%; | ||
| overflow-y: auto; | ||
| ` | ||
|
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| export function AutodetectPage() { | ||
| const { t } = useTranslationSafe() | ||
| // const minimizerIndex = useRecoilValue(minimizerIndexAtom) | ||
| const autodetectResults = useRecoilValue(autodetectResultsAtom) | ||
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| return ( | ||
| <Layout> | ||
| <Container> | ||
| <Row noGutters> | ||
| <Col> | ||
| <TableWrapper> | ||
| <Table striped> | ||
| <thead> | ||
| <tr> | ||
| <th>{'#'}</th> | ||
| <th>{t('Seq. name')}</th> | ||
| <th>{t('dataset')}</th> | ||
| <th>{t('total hits')}</th> | ||
| <th>{t('max hit')}</th> | ||
| </tr> | ||
| </thead> | ||
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| <tbody> | ||
| {autodetectResults.map((res) => ( | ||
| <tr key={res.fastaRecord.index}> | ||
| <td>{res.fastaRecord.index}</td> | ||
| <td>{res.fastaRecord.seqName}</td> | ||
| <td>{res.result.dataset ?? ''}</td> | ||
| <td>{res.result.totalHits}</td> | ||
| <td>{res.result.maxNormalizedHit.toFixed(3)}</td> | ||
| </tr> | ||
| ))} | ||
| </tbody> | ||
| </Table> | ||
| </TableWrapper> | ||
| </Col> | ||
| </Row> | ||
| </Container> | ||
| </Layout> | ||
| ) | ||
| } |
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58 changes: 58 additions & 0 deletions
58
packages_rs/nextclade-web/src/hooks/useRunSeqAutodetect.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| import { useRouter } from 'next/router' | ||
| import { NextcladeSeqAutodetectWasm } from 'src/gen/nextclade-wasm' | ||
| import { useRecoilCallback } from 'recoil' | ||
| import { ErrorInternal } from 'src/helpers/ErrorInternal' | ||
| import { axiosFetch } from 'src/io/axiosFetch' | ||
| import { autodetectResultAtom, autodetectResultsAtom, minimizerIndexAtom } from 'src/state/autodetect.state' | ||
| import { minimizerIndexVersionAtom } from 'src/state/dataset.state' | ||
| import { MinimizerIndexJson, MinimizerSearchRecord } from 'src/types' | ||
| import { qrySeqInputsStorageAtom } from 'src/state/inputs.state' | ||
| import { getQueryFasta } from 'src/workers/launchAnalysis' | ||
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| export function useRunSeqAutodetect() { | ||
| const router = useRouter() | ||
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| return useRecoilCallback( | ||
| ({ set, reset, snapshot: { getPromise } }) => | ||
| () => { | ||
| reset(minimizerIndexAtom) | ||
| reset(autodetectResultsAtom) | ||
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| void router.push('/autodetect', '/autodetect') // eslint-disable-line no-void | ||
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| function onResult(res: MinimizerSearchRecord) { | ||
| set(autodetectResultAtom(res.fastaRecord.index), res) | ||
| } | ||
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| Promise.all([getPromise(qrySeqInputsStorageAtom), getPromise(minimizerIndexVersionAtom)]) | ||
| .then(async ([qrySeqInputs, minimizerIndexVersion]) => { | ||
| if (!minimizerIndexVersion) { | ||
| throw new ErrorInternal('Tried to run minimizer search without minimizer index available') | ||
| } | ||
| const fasta = await getQueryFasta(qrySeqInputs) | ||
| const minimizerIndex: MinimizerIndexJson = await axiosFetch(minimizerIndexVersion.path) | ||
| set(minimizerIndexAtom, minimizerIndex) | ||
| return runAutodetect(fasta, minimizerIndex, onResult) | ||
| }) | ||
| .catch((error) => { | ||
| throw error | ||
| }) | ||
| }, | ||
| [router], | ||
| ) | ||
| } | ||
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| function runAutodetect( | ||
| fasta: string, | ||
| minimizerIndex: MinimizerIndexJson, | ||
| onResult: (res: MinimizerSearchRecord) => void, | ||
| ) { | ||
| const nextcladeAutodetect = NextcladeSeqAutodetectWasm.new(JSON.stringify(minimizerIndex)) | ||
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| function onResultParsed(resStr: string) { | ||
| const result = JSON.parse(resStr) as MinimizerSearchRecord | ||
| onResult(result) | ||
| } | ||
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| nextcladeAutodetect.autodetect(fasta, onResultParsed) | ||
| } |
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