@apollo-annotation/jbrowse-plugin-apollo 0.1.21 → 0.2.1

package/src/FeatureDetailsWidget/TranscriptBasic.tsx

@@ -3,71 +3,23 @@ import {
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
-import { AbstractSessionModel, revcom } from '@jbrowse/core/util'
-import { Typography } from '@mui/material'
+import { AbstractSessionModel, getFrame, revcom } from '@jbrowse/core/util'
+import {
+  Paper,
+  Typography,
+  Table,
+  TableBody,
+  TableCell,
+  TableContainer,
+  TableRow,
+  useTheme,
+} from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
 
 import { ApolloSessionModel } from '../session'
-import { CDSInfo } from './TranscriptSequence'
 import { NumberTextField } from './NumberTextField'
 
-interface ExonInfo {
-  min: number
-  max: number
-}
-
-/**
- * Get single feature by featureId
- * @param feature -
- * @param featureId -
- * @returns
- */
-function getFeatureFromId(
-  feature: AnnotationFeature,
-  featureId: string,
-): 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
-  }
-  for (const [, childFeature] of feature.children) {
-    const subFeature = getFeatureFromId(childFeature, featureId)
-    if (subFeature) {
-      return subFeature
-    }
-  }
-  return
-}
-
-function findExonInRange(
-  exons: ExonInfo[],
-  pairStart: number,
-  pairEnd: number,
-): ExonInfo | null {
-  for (const exon of exons) {
-    if (Number(exon.min) <= pairStart && Number(exon.max) >= pairEnd) {
-      return exon
-    }
-  }
-  return null
-}
-
-function removeMatchingExon(
-  exons: ExonInfo[],
-  matchStart: number,
-  matchEnd: number,
-): ExonInfo[] {
-  // Filter the array to remove elements matching the specified start and end
-  return exons.filter(
-    (exon) => !(exon.min === matchStart && exon.max === matchEnd),
-  )
-}
-
 export const TranscriptBasicInformation = observer(
   function TranscriptBasicInformation({
     assembly,
@@ -84,362 +36,159 @@ export const TranscriptBasicInformation = observer(
     const currentAssembly = session.apolloDataStore.assemblies.get(assembly)
     const refData = currentAssembly?.getByRefName(refName)
     const { changeManager } = session.apolloDataStore
+    const theme = useTheme()
 
-    function handleStartChange(
-      newStart: number,
-      featureId: string,
-      oldStart: number,
+    function handleLocationChange(
+      oldLocation: number,
+      newLocation: number,
+      feature: AnnotationFeature,
+      isMin: boolean,
     ) {
-      newStart--
-      oldStart--
-      if (newStart < feature.min) {
-        notify('Feature start cannot be less than parent starts', 'error')
-        return
-      }
-      const subFeature = getFeatureFromId(feature, featureId)
-      if (!subFeature?.children) {
-        return
+      if (!feature.children) {
+        throw new Error('Transcript should have child features')
       }
-      // 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
-        ) {
+      for (const [, child] of feature.children) {
+        if (isMin && oldLocation - 1 === child.min) {
           const change = new LocationStartChange({
             typeName: 'LocationStartChange',
-            changedIds: [child[1]._id],
-            featureId,
-            oldStart,
-            newStart,
+            changedIds: [child._id],
+            featureId: feature._id,
+            oldStart: oldLocation - 1,
+            newStart: newLocation - 1,
             assembly,
           })
           changeManager.submit(change).catch(() => {
             notify('Error updating feature start position', 'error')
           })
+          return
         }
-      }
-      return
-    }
-
-    function handleEndChange(
-      newEnd: number,
-      featureId: string,
-      oldEnd: number,
-    ) {
-      const subFeature = getFeatureFromId(feature, featureId)
-      if (newEnd > feature.max) {
-        notify('Feature start cannot be greater than parent end', 'error')
-        return
-      }
-      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
-        ) {
+        if (!isMin && newLocation === child.max) {
           const change = new LocationEndChange({
             typeName: 'LocationEndChange',
-            changedIds: [child[1]._id],
-            featureId,
-            oldEnd,
-            newEnd,
+            changedIds: [child._id],
+            featureId: feature._id,
+            oldEnd: child.max,
+            newEnd: newLocation,
             assembly,
           })
           changeManager.submit(change).catch(() => {
-            notify('Error updating feature end position', 'error')
+            notify('Error updating feature start position', 'error')
           })
+          return
         }
       }
-      return
     }
 
-    const featureNew = feature
-    let exonsArray: ExonInfo[] = []
-    const traverse = (currentFeature: AnnotationFeature) => {
-      if (currentFeature.type === 'exon') {
-        exonsArray.push({
-          min: currentFeature.min + 1,
-          max: currentFeature.max,
-        })
-      }
-      if (currentFeature.children) {
-        for (const child of currentFeature.children) {
-          traverse(child[1])
-        }
-      }
+    if (!refData) {
+      return null
     }
-    traverse(featureNew)
-
-    const CDSresult: CDSInfo[] = []
-    const CDSData = featureNew.cdsLocations
-    if (refData) {
-      for (const CDSDatum of CDSData) {
-        for (const dataPoint of CDSDatum) {
-          let startSeq = refData.getSequence(
-            Number(dataPoint.min) - 2,
-            Number(dataPoint.min),
-          )
-          let endSeq = refData.getSequence(
-            Number(dataPoint.max),
-            Number(dataPoint.max) + 2,
-          )
-
-          if (featureNew.strand === -1 && startSeq && endSeq) {
-            startSeq = revcom(startSeq)
-            endSeq = revcom(endSeq)
-          }
-          const oneCDS: CDSInfo = {
-            id: featureNew._id,
-            type: 'CDS',
-            strand: Number(featureNew.strand),
-            min: dataPoint.min + 1,
-            max: dataPoint.max,
-            oldMin: dataPoint.min + 1,
-            oldMax: dataPoint.max,
-            startSeq,
-            endSeq,
-          }
-          // CDSresult.push(oneCDS)
-          // Check if there is already an object with the same start and end
-          const exists = CDSresult.some(
-            (obj) =>
-              obj.min === oneCDS.min &&
-              obj.max === oneCDS.max &&
-              obj.type === oneCDS.type,
-          )
 
-          // If no such object exists, add the new object to the array
-          if (!exists) {
-            CDSresult.push(oneCDS)
-          }
-
-          // Add possible UTRs
-          const foundExon = findExonInRange(
-            exonsArray,
-            dataPoint.min + 1,
-            dataPoint.max,
-          )
-          if (foundExon && Number(foundExon.min) < dataPoint.min) {
-            if (feature.strand === 1) {
-              const oneCDS: CDSInfo = {
-                id: feature._id,
-                type: 'five_prime_UTR',
-                strand: Number(feature.strand),
-                min: foundExon.min,
-                max: dataPoint.min,
-                oldMin: foundExon.min,
-                oldMax: dataPoint.min,
-                startSeq: '',
-                endSeq: '',
-              }
-              CDSresult.push(oneCDS)
-            } else {
-              const oneCDS: CDSInfo = {
-                id: feature._id,
-                type: 'three_prime_UTR',
-                strand: Number(feature.strand),
-                min: dataPoint.min + 1,
-                max: foundExon.min + 1,
-                oldMin: dataPoint.min + 1,
-                oldMax: foundExon.min + 1,
-                startSeq: '',
-                endSeq: '',
-              }
-              CDSresult.push(oneCDS)
+    const { strand, transcriptParts } = feature
+    const [firstLocation] = transcriptParts
+
+    const locationData = firstLocation
+      .map((loc, idx) => {
+        const { max, min, type } = loc
+        let label: string = type
+        if (label === 'threePrimeUTR') {
+          label = '3` UTR'
+        } else if (label === 'fivePrimeUTR') {
+          label = '5` UTR'
+        }
+        let fivePrimeSpliceSite
+        let threePrimeSpliceSite
+        let frameColor
+        if (type === 'CDS') {
+          const { phase } = loc
+          const frame = getFrame(min, max, strand ?? 1, phase)
+          frameColor = theme.palette.framesCDS.at(frame)?.main
+          const previousLoc = firstLocation.at(idx - 1)
+          const nextLoc = firstLocation.at(idx + 1)
+          if (strand === 1) {
+            if (previousLoc?.type === 'intron') {
+              fivePrimeSpliceSite = refData.getSequence(min - 2, min)
             }
-            exonsArray = removeMatchingExon(
-              exonsArray,
-              foundExon.min,
-              foundExon.max,
-            )
-          }
-          if (foundExon && Number(foundExon.max) > dataPoint.max) {
-            if (feature.strand === 1) {
-              const oneCDS: CDSInfo = {
-                id: feature._id,
-                type: 'three_prime_UTR',
-                strand: Number(feature.strand),
-                min: dataPoint.max + 1,
-                max: foundExon.max,
-                oldMin: dataPoint.max + 1,
-                oldMax: foundExon.max,
-                startSeq: '',
-                endSeq: '',
-              }
-              CDSresult.push(oneCDS)
-            } else {
-              const oneCDS: CDSInfo = {
-                id: feature._id,
-                type: 'five_prime_UTR',
-                strand: Number(feature.strand),
-                min: dataPoint.min + 1,
-                max: foundExon.max,
-                oldMin: dataPoint.min + 1,
-                oldMax: foundExon.max,
-                startSeq: '',
-                endSeq: '',
-              }
-              CDSresult.push(oneCDS)
+            if (nextLoc?.type === 'intron') {
+              threePrimeSpliceSite = refData.getSequence(max, max + 2)
+            }
+          } else {
+            if (previousLoc?.type === 'intron') {
+              fivePrimeSpliceSite = revcom(refData.getSequence(max, max + 2))
+            }
+            if (nextLoc?.type === 'intron') {
+              threePrimeSpliceSite = revcom(refData.getSequence(min - 2, min))
             }
-            exonsArray = removeMatchingExon(
-              exonsArray,
-              foundExon.min,
-              foundExon.max,
-            )
-          }
-          if (
-            dataPoint.min + 1 === foundExon?.min &&
-            dataPoint.max === foundExon.max
-          ) {
-            exonsArray = removeMatchingExon(
-              exonsArray,
-              foundExon.min,
-              foundExon.max,
-            )
           }
         }
-      }
-    }
-
-    // Add remaining UTRs if any
-    if (exonsArray.length > 0) {
-      // eslint-disable-next-line unicorn/no-array-for-each
-      exonsArray.forEach((element: ExonInfo) => {
-        if (featureNew.strand === 1) {
-          const oneCDS: CDSInfo = {
-            id: featureNew._id,
-            type: 'five_prime_UTR',
-            strand: Number(featureNew.strand),
-            min: element.min + 1,
-            max: element.max,
-            oldMin: element.min + 1,
-            oldMax: element.max,
-            startSeq: '',
-            endSeq: '',
-          }
-          CDSresult.push(oneCDS)
-        } else {
-          const oneCDS: CDSInfo = {
-            id: featureNew._id,
-            type: 'three_prime_UTR',
-            strand: Number(featureNew.strand),
-            min: element.min + 1,
-            max: element.max + 1,
-            oldMin: element.min + 1,
-            oldMax: element.max + 1,
-            startSeq: '',
-            endSeq: '',
-          }
-          CDSresult.push(oneCDS)
+        return {
+          min,
+          max,
+          label,
+          fivePrimeSpliceSite,
+          threePrimeSpliceSite,
+          frameColor,
         }
-        exonsArray = removeMatchingExon(exonsArray, element.min, element.max)
       })
-    }
-
-    CDSresult.sort((a, b) => {
-      // Primary sorting by 'start' property
-      const startDifference = Number(a.min) - Number(b.min)
-      if (startDifference !== 0) {
-        return startDifference
-      }
-      return Number(a.max) - Number(b.max)
-    })
-    if (CDSresult.length > 0) {
-      CDSresult[0].startSeq = ''
-
-      // eslint-disable-next-line unicorn/prefer-at
-      CDSresult[CDSresult.length - 1].endSeq = ''
-
-      // Loop through the array and clear "startSeq" or "endSeq" based on the conditions
-      for (let i = 0; i < CDSresult.length; i++) {
-        if (i > 0 && CDSresult[i].min === CDSresult[i - 1].max) {
-          // Clear "startSeq" if the current item's "start" is equal to the previous item's "end"
-          CDSresult[i].startSeq = ''
-        }
-        if (
-          i < CDSresult.length - 1 &&
-          CDSresult[i].max === CDSresult[i + 1].min
-        ) {
-          // Clear "endSeq" if the next item's "start" is equal to the current item's "end"
-          CDSresult[i].endSeq = ''
-        }
-      }
-    }
-
-    const transcriptItems = CDSresult
+      .filter((loc) => loc.label !== 'intron')
 
     return (
       <>
-        <Typography
-          variant="h5"
-          style={{ marginLeft: '15px', marginBottom: '0' }}
-        >
-          CDS and UTRs
+        <Typography variant="h5">Structure</Typography>
+        <Typography variant="h6">
+          {strand === 1 ? 'Forward' : 'Reverse'} strand
         </Typography>
-        <div>
-          {transcriptItems.map((item, index) => (
-            <div key={index} style={{ display: 'flex', alignItems: 'center' }}>
-              <span style={{ marginLeft: '20px', width: '50px' }}>
-                {item.type === 'three_prime_UTR'
-                  ? '3 UTR'
-                  : // eslint-disable-next-line unicorn/no-nested-ternary
-                    item.type === 'five_prime_UTR'
-                    ? '5 UTR'
-                    : 'CDS'}
-              </span>
-              <span style={{ fontWeight: 'bold', width: '30px' }}>
-                {item.startSeq}
-              </span>
-              <NumberTextField
-                margin="dense"
-                id={item.id}
-                disabled={item.type !== 'CDS'}
-                style={{
-                  width: '150px',
-                  marginLeft: '8px',
-                  backgroundColor:
-                    item.startSeq.trim() === '' && index !== 0
-                      ? 'lightblue'
-                      : 'inherit',
-                }}
-                variant="outlined"
-                value={item.min}
-                onChangeCommitted={(newStart: number) => {
-                  handleStartChange(newStart, item.id, Number(item.oldMin))
-                }}
-              />
-              <span style={{ margin: '0 10px' }}>
-                {/* eslint-disable-next-line unicorn/no-nested-ternary */}
-                {item.strand === -1 ? '-' : item.strand === 1 ? '+' : ''}
-              </span>
-              <NumberTextField
-                margin="dense"
-                id={item.id}
-                disabled={item.type !== 'CDS'}
-                style={{
-                  width: '150px',
-                  backgroundColor:
-                    item.endSeq.trim() === '' &&
-                    index + 1 !== transcriptItems.length
-                      ? 'lightblue'
-                      : 'inherit',
-                }}
-                variant="outlined"
-                value={item.max}
-                onChangeCommitted={(newEnd: number) => {
-                  handleEndChange(newEnd, item.id, Number(item.oldMax))
-                }}
-              />
-              <span style={{ marginLeft: '8px', fontWeight: 'bold' }}>
-                {item.endSeq}
-              </span>
-            </div>
-          ))}
-        </div>
+        <TableContainer component={Paper}>
+          <Table size="small">
+            <TableBody>
+              {locationData.map((loc) => (
+                <TableRow key={`${loc.label}:${loc.min}-${loc.max}`}>
+                  <TableCell
+                    component="th"
+                    scope="row"
+                    style={{ background: loc.frameColor }}
+                  >
+                    {loc.label}
+                  </TableCell>
+                  <TableCell>{loc.fivePrimeSpliceSite ?? ''}</TableCell>
+                  <TableCell padding="none">
+                    <NumberTextField
+                      margin="dense"
+                      variant="outlined"
+                      value={strand === 1 ? loc.min + 1 : loc.max}
+                      onChangeCommitted={(newLocation: number) => {
+                        handleLocationChange(
+                          strand === 1 ? loc.min + 1 : loc.max,
+                          newLocation,
+                          feature,
+                          strand === 1,
+                        )
+                      }}
+                    />
+                    {/* {strand === 1 ? loc.min : loc.max} */}
+                  </TableCell>
+                  <TableCell padding="none">
+                    <NumberTextField
+                      margin="dense"
+                      // disabled={item.type !== 'CDS'}
+                      variant="outlined"
+                      value={strand === 1 ? loc.max : loc.min + 1}
+                      onChangeCommitted={(newLocation: number) => {
+                        handleLocationChange(
+                          strand === 1 ? loc.max : loc.min + 1,
+                          newLocation,
+                          feature,
+                          strand !== 1,
+                        )
+                      }}
+                    />
+                    {/* {strand === 1 ? loc.max : loc.min} */}
+                  </TableCell>
+                  <TableCell>{loc.threePrimeSpliceSite ?? ''}</TableCell>
+                </TableRow>
+              ))}
+            </TableBody>
+          </Table>
+        </TableContainer>
       </>
     )
   },