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@shashankbrgowda
shashankbrgowda committed Aug 15, 2024
2 parents 688fbf3 + 5146ddc commit 0e92a72
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Showing 17 changed files with 945 additions and 1,163 deletions.
2 changes: 1 addition & 1 deletion packages/apollo-mst/src/AnnotationFeatureModel.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ export const AnnotationFeatureModel = types
/**
* Type of feature. Can be any string, but is usually an ontology term,
* e.g. "gene" from the
* {@link http://sequenceontology.org/browser/current_release/term/SO:0005855 |Sequence Ontology}.
* {@link http://sequenceontology.org/browser/current_release/term/SO:0000704 |Sequence Ontology}.
*/
type: types.string,
/**
Expand Down
146 changes: 70 additions & 76 deletions packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
/* eslint-disable @typescript-eslint/no-explicit-any */
import { AnnotationFeature } from '@apollo-annotation/mst'
import {
LocationEndChange,
Expand All @@ -22,22 +21,22 @@ import { NumberTextField } from './NumberTextField'
function getFeatureFromId(
feature: AnnotationFeature,
featureId: string,
): AnnotationFeature | null {
): AnnotationFeature | undefined {
if (feature._id === featureId) {
return feature
}
// Check if there is also childFeatures in parent feature and it's not empty
// Let's get featureId from recursive method
if (!feature.children) {
return null
return
}
for (const [, childFeature] of feature.children) {
const subFeature = getFeatureFromId(childFeature, featureId)
if (subFeature) {
return subFeature
}
}
return null
return
}

function findExonInRange(
Expand Down Expand Up @@ -80,7 +79,6 @@ export const TranscriptBasicInformation = observer(
const currentAssembly = session.apolloDataStore.assemblies.get(assembly)
const refData = currentAssembly?.getByRefName(refName)
const { changeManager } = session.apolloDataStore
const fea = feature as unknown as AnnotationFeature

function handleStartChange(
newStart: number,
Expand All @@ -89,33 +87,31 @@ export const TranscriptBasicInformation = observer(
) {
newStart--
oldStart--
if (newStart < fea.min) {
if (newStart < feature.min) {
notify('Feature start cannot be less than parent starts', 'error')
return
}
const subFeature = getFeatureFromId(
fea,
featureId,
) as unknown as AnnotationFeature
if (subFeature.children) {
// Let's check CDS start and end values. And possibly update those too
for (const child of subFeature.children) {
if (
(child[1].type === 'CDS' || child[1].type === 'exon') &&
child[1].min === oldStart
) {
const change = new LocationStartChange({
typeName: 'LocationStartChange',
changedIds: [child[1]._id],
featureId,
oldStart,
newStart,
assembly,
})
changeManager.submit(change).catch(() => {
notify('Error updating feature start position')
})
}
const subFeature = getFeatureFromId(feature, featureId)
if (!subFeature?.children) {
return
}
// Let's check CDS start and end values. And possibly update those too
for (const child of subFeature.children) {
if (
(child[1].type === 'CDS' || child[1].type === 'exon') &&
child[1].min === oldStart
) {
const change = new LocationStartChange({
typeName: 'LocationStartChange',
changedIds: [child[1]._id],
featureId,
oldStart,
newStart,
assembly,
})
changeManager.submit(change).catch(() => {
notify('Error updating feature start position', 'error')
})
}
}
}
Expand All @@ -126,34 +122,35 @@ export const TranscriptBasicInformation = observer(
oldEnd: number,
) {
const subFeature = getFeatureFromId(feature, featureId)
if (newEnd > fea.max) {
if (newEnd > feature.max) {
notify('Feature start cannot be greater than parent end', 'error')
return
}
if (subFeature?.children) {
// Let's check CDS start and end values. And possibly update those too
for (const child of subFeature.children) {
if (
(child[1].type === 'CDS' || child[1].type === 'exon') &&
child[1].max === oldEnd
) {
const change = new LocationEndChange({
typeName: 'LocationEndChange',
changedIds: [child[1]._id],
featureId,
oldEnd,
newEnd,
assembly,
})
changeManager.submit(change).catch(() => {
notify('Error updating feature end position')
})
}
if (!subFeature?.children) {
return
}
// Let's check CDS start and end values. And possibly update those too
for (const child of subFeature.children) {
if (
(child[1].type === 'CDS' || child[1].type === 'exon') &&
child[1].max === oldEnd
) {
const change = new LocationEndChange({
typeName: 'LocationEndChange',
changedIds: [child[1]._id],
featureId,
oldEnd,
newEnd,
assembly,
})
changeManager.submit(change).catch(() => {
notify('Error updating feature end position', 'error')
})
}
}
}

const featureNew = feature as unknown as AnnotationFeature
const featureNew = feature
let exonsArray: ExonInfo[] = []
const traverse = (currentFeature: AnnotationFeature) => {
if (currentFeature.type === 'exon') {
Expand Down Expand Up @@ -196,8 +193,8 @@ export const TranscriptBasicInformation = observer(
max: dataPoint.max as unknown as string,
oldMin: (dataPoint.min + 1) as unknown as string,
oldMax: dataPoint.max as unknown as string,
startSeq: startSeq || '',
endSeq: endSeq || '',
startSeq,
endSeq,
}
// CDSresult.push(oneCDS)
// Check if there is already an object with the same start and end
Expand Down Expand Up @@ -226,9 +223,9 @@ export const TranscriptBasicInformation = observer(
type: 'five_prime_UTR',
strand: Number(feature.strand),
min: foundExon.min,
max: dataPoint.min as unknown as string,
max: String(dataPoint.min),
oldMin: foundExon.min,
oldMax: dataPoint.min as unknown as string,
oldMax: String(dataPoint.min),
startSeq: '',
endSeq: '',
}
Expand All @@ -238,12 +235,10 @@ export const TranscriptBasicInformation = observer(
id: feature._id,
type: 'three_prime_UTR',
strand: Number(feature.strand),
min: (dataPoint.min + 1) as unknown as string,
max: ((foundExon.min as unknown as number) +
1) as unknown as string,
oldMin: (dataPoint.min + 1) as unknown as string,
oldMax: ((foundExon.min as unknown as number) +
1) as unknown as string,
min: dataPoint.min + 1,
max: foundExon.min + 1,

Check failure on line 239 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
oldMin: dataPoint.min + 1,
oldMax: foundExon.min + 1,

Check failure on line 241 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
startSeq: '',
endSeq: '',
}
Expand All @@ -261,9 +256,9 @@ export const TranscriptBasicInformation = observer(
id: feature._id,
type: 'three_prime_UTR',
strand: Number(feature.strand),
min: (dataPoint.max + 1) as unknown as string,
min: dataPoint.max + 1,
max: foundExon.max,
oldMin: (dataPoint.max + 1) as unknown as string,
oldMin: dataPoint.max + 1,
oldMax: foundExon.max,
startSeq: '',
endSeq: '',
Expand All @@ -274,9 +269,9 @@ export const TranscriptBasicInformation = observer(
id: feature._id,
type: 'five_prime_UTR',
strand: Number(feature.strand),
min: (dataPoint.min + 1) as unknown as string,
min: dataPoint.min + 1,
max: foundExon.max,
oldMin: (dataPoint.min + 1) as unknown as string,
oldMin: dataPoint.min + 1,
oldMax: foundExon.max,
startSeq: '',
endSeq: '',
Expand All @@ -295,8 +290,8 @@ export const TranscriptBasicInformation = observer(
) {
exonsArray = removeMatchingExon(
exonsArray,
foundExon?.min as unknown as string,
foundExon?.max as unknown as string,
foundExon?.min,
foundExon?.max,
)
}
}
Expand All @@ -312,10 +307,9 @@ export const TranscriptBasicInformation = observer(
id: featureNew._id,
type: 'five_prime_UTR',
strand: Number(featureNew.strand),
min: ((element.min as unknown as number) + 1) as unknown as string,
min: element.min + 1,

Check failure on line 310 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
max: element.max,
oldMin: ((element.min as unknown as number) +
1) as unknown as string,
oldMin: element.min + 1,

Check failure on line 312 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
oldMax: element.max,
startSeq: '',
endSeq: '',
Expand All @@ -326,12 +320,10 @@ export const TranscriptBasicInformation = observer(
id: featureNew._id,
type: 'three_prime_UTR',
strand: Number(featureNew.strand),
min: ((element.min as unknown as number) + 1) as unknown as string,
max: ((element.max as unknown as number) + 1) as unknown as string,
oldMin: ((element.min as unknown as number) +
1) as unknown as string,
oldMax: ((element.max as unknown as number) +
1) as unknown as string,
min: element.min + 1,

Check failure on line 323 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
max: element.max + 1,

Check failure on line 324 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
oldMin: element.min + 1,

Check failure on line 325 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
oldMax: element.max + 1,

Check failure on line 326 in packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

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GitHub Actions / Lint 

Operands of '+' operations must be a number or string. Got `string` + `number`
startSeq: '',
endSeq: '',
}
Expand Down Expand Up @@ -387,7 +379,8 @@ export const TranscriptBasicInformation = observer(
<span style={{ marginLeft: '20px', width: '50px' }}>
{item.type === 'three_prime_UTR'
? '3 UTR'
: item.type === 'five_prime_UTR'
: // eslint-disable-next-line unicorn/no-nested-ternary
item.type === 'five_prime_UTR'
? '5 UTR'
: 'CDS'}
</span>
Expand All @@ -413,6 +406,7 @@ export const TranscriptBasicInformation = observer(
}}
/>
<span style={{ margin: '0 10px' }}>
{/* eslint-disable-next-line unicorn/no-nested-ternary */}
{item.strand === -1 ? '-' : item.strand === 1 ? '+' : ''}
</span>
<NumberTextField
Expand Down
2 changes: 1 addition & 1 deletion packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/index.ts
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
export { ApolloFeatureDetailsWidget } from './ApolloFeatureDetailsWidget'
export { ApolloFeatureDetailsWidgetModel } from './model'
export { ApolloTranscriptDetailsWidget } from './ApolloTranscriptDetailsWidget'
export { ApolloTranscriptDetails } from './model'
export { ApolloTranscriptDetailsModel } from './model'
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