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feat(web): display relative substitutions in nuc sequence view
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packages/nextclade-web/src/components/SequenceView/SequenceViewAbsolute.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| import type { AnalysisResult } from 'src/types' | ||
| import React from 'react' | ||
| import { useRecoilValue } from 'recoil' | ||
| import { SequenceMarkerAmbiguous } from 'src/components/SequenceView/SequenceMarkerAmbiguous' | ||
| import { useTranslationSafe } from 'src/helpers/useTranslationSafe' | ||
| import { maxNucMarkersAtom } from 'src/state/seqViewSettings.state' | ||
| import { genomeSizeAtom } from 'src/state/results.state' | ||
| import { SequenceMarkerGap } from './SequenceMarkerGap' | ||
| import { SequenceMarkerMissing } from './SequenceMarkerMissing' | ||
| import { SequenceMarkerMutation } from './SequenceMarkerMutation' | ||
| import { SequenceMarkerUnsequencedEnd, SequenceMarkerUnsequencedStart } from './SequenceMarkerUnsequenced' | ||
| import { SequenceMarkerFrameShift } from './SequenceMarkerFrameShift' | ||
| import { SequenceMarkerInsertion } from './SequenceMarkerInsertion' | ||
|
|
||
| export interface SequenceViewAbsoluteProps { | ||
| sequence: AnalysisResult | ||
| width: number | ||
| } | ||
|
|
||
| export function SequenceViewAbsolute({ sequence, width }: SequenceViewAbsoluteProps) { | ||
| const { | ||
| index, | ||
| seqName, | ||
| substitutions, | ||
| missing, | ||
| deletions, | ||
| alignmentRange, | ||
| frameShifts, | ||
| insertions, | ||
| nucToAaMuts, | ||
| nonACGTNs, | ||
| } = sequence | ||
|
|
||
| const { t } = useTranslationSafe() | ||
| const maxNucMarkers = useRecoilValue(maxNucMarkersAtom) | ||
|
|
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| const genomeSize = useRecoilValue(genomeSizeAtom) | ||
|
|
||
| const pixelsPerBase = width / genomeSize | ||
|
|
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| const mutationViews = substitutions.map((substitution) => { | ||
| return ( | ||
| <SequenceMarkerMutation | ||
| key={substitution.pos} | ||
| index={index} | ||
| seqName={seqName} | ||
| substitution={substitution} | ||
| nucToAaMuts={nucToAaMuts} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| ) | ||
| }) | ||
|
|
||
| const missingViews = missing.map((oneMissing) => { | ||
| return ( | ||
| <SequenceMarkerMissing | ||
| key={oneMissing.range.begin} | ||
| index={index} | ||
| seqName={seqName} | ||
| missing={oneMissing} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| ) | ||
| }) | ||
|
|
||
| const ambigViews = nonACGTNs.map((ambig) => { | ||
| return ( | ||
| <SequenceMarkerAmbiguous | ||
| key={ambig.range.begin} | ||
| index={index} | ||
| seqName={seqName} | ||
| ambiguous={ambig} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| ) | ||
| }) | ||
|
|
||
| const deletionViews = deletions.map((deletion) => { | ||
| return ( | ||
| <SequenceMarkerGap | ||
| key={deletion.range.begin} | ||
| index={index} | ||
| seqName={seqName} | ||
| deletion={deletion} | ||
| nucToAaMuts={nucToAaMuts} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| ) | ||
| }) | ||
|
|
||
| const insertionViews = insertions.map((insertion) => { | ||
| return ( | ||
| <SequenceMarkerInsertion | ||
| key={insertion.pos} | ||
| index={index} | ||
| seqName={seqName} | ||
| insertion={insertion} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| ) | ||
| }) | ||
|
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||
| const frameShiftMarkers = frameShifts.map((frameShift) => ( | ||
| <SequenceMarkerFrameShift | ||
| key={`${frameShift.cdsName}_${frameShift.nucAbs.map((na) => na.begin).join('-')}`} | ||
| index={index} | ||
| seqName={seqName} | ||
| frameShift={frameShift} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| )) | ||
|
|
||
| const totalMarkers = | ||
| mutationViews.length + deletionViews.length + missingViews.length + frameShiftMarkers.length + insertionViews.length | ||
| if (totalMarkers > maxNucMarkers) { | ||
| return ( | ||
| <p | ||
| title={t( | ||
| "Markers are the colored rectangles which represent mutations, deletions etc. There is a technical limit of how many of those can be displayed at a time, depending on how fast your computer is. You can tune the threshold in the 'Settings' dialog, accessible with the button on the top panel.", | ||
| )} | ||
| > | ||
| {t( | ||
| 'Too many markers to display ({{totalMarkers}}). The threshold ({{maxNucMarkers}}) can be increased in "Settings" dialog', | ||
| { totalMarkers, maxNucMarkers }, | ||
| )} | ||
| </p> | ||
| ) | ||
| } | ||
|
|
||
| return ( | ||
| <> | ||
| <rect fill="transparent" x={0} y={-10} width={genomeSize} height="30" /> | ||
| <SequenceMarkerUnsequencedStart | ||
| index={index} | ||
| seqName={seqName} | ||
| alignmentStart={alignmentRange.begin} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| {mutationViews} | ||
| {missingViews} | ||
| {ambigViews} | ||
| {deletionViews} | ||
| {insertionViews} | ||
| <SequenceMarkerUnsequencedEnd | ||
| index={index} | ||
| seqName={seqName} | ||
| genomeSize={genomeSize} | ||
| alignmentEnd={alignmentRange.end} | ||
| pixelsPerBase={pixelsPerBase} | ||
| /> | ||
| {frameShiftMarkers} | ||
| </> | ||
| ) | ||
| } |
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