@apollo-annotation/shared 1.0.1 → 1.1.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "1.0.1",
+  "version": "1.1.0",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
@@ -17,19 +17,19 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^1.0.1",
-    "@apollo-annotation/mst": "^1.0.1",
-    "@apollo-annotation/schemas": "^1.0.1",
+    "@apollo-annotation/common": "^1.1.0",
+    "@apollo-annotation/mst": "^1.1.0",
+    "@apollo-annotation/schemas": "^1.1.0",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/core": "^4.3.0",
     "bson-objectid": "^2.0.4",
     "generic-filehandle2": "^2.0.18",
     "jwt-decode": "^3.1.2",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
@@ -46,8 +46,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",

package/src/Changes/MergeAndUndoMergeTranscriptsChanges.ts

@@ -129,9 +129,7 @@ export class MergeTranscriptsChange extends FeatureChange {
     secondFeatureChild: AnnotationFeatureSnapshot,
     firstTranscript: Feature,
   ) {
-    if (!firstTranscript.children) {
-      firstTranscript.children = new Map<string, Feature>()
-    }
+    firstTranscript.children ??= new Map<string, Feature>()
     let merged = false
     let mrgChild: Feature | undefined
     let toDelete
@@ -169,9 +167,7 @@ export class MergeTranscriptsChange extends FeatureChange {
           firstFeatureChild.max,
         )
 
-        if (!mrgChild.attributes) {
-          mrgChild.attributes = {}
-        }
+        mrgChild.attributes ??= {}
 
         const mrgChildAttr: Record<string, string[]> = JSON.parse(
           JSON.stringify(mrgChild.attributes),
@@ -256,9 +252,7 @@ export class MergeTranscriptsChange extends FeatureChange {
     secondFeatureChild: AnnotationFeatureSnapshot,
     firstTranscript: AnnotationFeature,
   ) {
-    if (!firstTranscript.children) {
-      firstTranscript.children = new Map<string, AnnotationFeature>()
-    }
+    firstTranscript.children ??= new Map<string, AnnotationFeature>()
     let merged = false
     let mrgChild: AnnotationFeature | undefined
     let toDelete

package/src/Checks/CDSCheck.ts

@@ -104,8 +104,8 @@ function getOriginalCodonLocation(
       ? cdsLocation.toSorted((a, b) => (a.min < b.min ? 1 : -1))
       : cdsLocation.toSorted((a, b) => (a.min < b.min ? -1 : 1))
   let i = 0
-  let currentStart: number | undefined = undefined
-  let currentEnd: number | undefined = undefined
+  let currentStart: number | undefined
+  let currentEnd: number | undefined
   for (let iloc = 0; iloc < sortedLocation.length; iloc++) {
     const loc = sortedLocation[iloc]
     const { phase } = loc
@@ -172,7 +172,7 @@ async function checkMRNA(
           name: CHECK_NAME,
           cause: CAUSES[CAUSES.MissingStartCodon],
           ids,
-          refSeq: refSeq.toString(),
+          refSeq,
           start: cdsStart,
           end: cdsStart,
           message: `Unexpected start codon "${start_codon}" in feature "${getPrintableId(feature)}": `,
@@ -186,7 +186,7 @@ async function checkMRNA(
           name: CHECK_NAME,
           cause: CAUSES[CAUSES.MissingStopCodon],
           ids,
-          refSeq: refSeq.toString(),
+          refSeq,
           start: cdsEnd,
           end: cdsEnd,
           message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
@@ -198,7 +198,7 @@ async function checkMRNA(
         name: CHECK_NAME,
         cause: CAUSES[CAUSES.MissingStopCodon],
         ids,
-        refSeq: refSeq.toString(),
+        refSeq,
         start: cdsEnd,
         end: cdsEnd,
         message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
@@ -217,7 +217,7 @@ async function checkMRNA(
           name: CHECK_NAME,
           cause: CAUSES[CAUSES.InternalStopCodon],
           ids,
-          refSeq: refSeq.toString(),
+          refSeq,
           start: codonStart,
           end: codonEnd,
           message: `Internal stop codon in feature "${getPrintableId(feature)}"`,

package/src/Checks/TranscriptCheck.ts

@@ -78,7 +78,7 @@ async function checkTranscript(
         name: CHECK_NAME,
         cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtFivePrime],
         ids: [feature._id],
-        refSeq: feature.refSeq.toString(),
+        refSeq: feature.refSeq,
         start: spliceSequence.fivePrimeMin,
         end: spliceSequence.fivePrimeMin + 2,
         message: `Unexpected 5′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
@@ -92,7 +92,7 @@ async function checkTranscript(
         name: CHECK_NAME,
         cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
         ids: [feature._id],
-        refSeq: feature.refSeq.toString(),
+        refSeq: feature.refSeq,
         start: spliceSequence.threePrimeMin,
         end: spliceSequence.threePrimeMin + 2,
         message: `Unexpected 3′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,

package/src/Checks/util.ts

@@ -3,11 +3,11 @@ import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 export function getPrintableId(feature: AnnotationFeatureSnapshot): string {
   const gff_id = feature.attributes?.gff_id?.join(', ')
   if (gff_id) {
-    return `${gff_id} (_id: ${feature._id.toString()})`
+    return `${gff_id} (_id: ${feature._id})`
   }
   const gff_name = feature.attributes?.gff_name?.join(', ')
   if (gff_name) {
-    return `${gff_name} (_id: ${feature._id.toString()})`
+    return `${gff_name} (_id: ${feature._id})`
   }
-  return `_id: ${feature._id.toString()}`
+  return `_id: ${feature._id}`
 }

package/src/GFF3/annotationFeatureToGFF3.test.ts

@@ -160,7 +160,7 @@ describe('annotationFeatureToGFF3', () => {
     const [mrna] = children
     const cds10001 = mrna.child_features.filter((child) => {
       const id = child[0].attributes?.ID
-      return id !== undefined && id[0] === 'cds10001'
+      return id?.[0] === 'cds10001'
     })
     assert.deepEqual(cds10001.length, 2)
 
@@ -185,7 +185,7 @@ describe('annotationFeatureToGFF3', () => {
 
     const cds10004 = mrna.child_features.filter((child) => {
       const id = child[0].attributes?.ID
-      return id !== undefined && id[0] === 'cds10004'
+      return id?.[0] === 'cds10004'
     })
     assert.deepEqual(cds10004.length, 2)
     const cds4_1 = cds10004[0][0]

package/src/GFF3/annotationFeatureToGFF3.ts

@@ -96,8 +96,8 @@ export function annotationFeatureToGFF3(
     }
 
     return {
-      start: Number(featureLoc.min) + 1,
-      end: Number(featureLoc.max),
+      start: featureLoc.min + 1,
+      end: featureLoc.max,
       seq_id: refSeqNames
         ? refSeqNames[featureLoc.refSeq] ?? null
         : featureLoc.refSeq,
@@ -261,7 +261,7 @@ function getTranscriptParts(
 function getCdsLocations(
   feature: AnnotationFeatureSnapshot,
 ): TranscriptPartCoding[][] {
-  let transcriptParts: TranscriptParts[] = []
+  let transcriptParts: TranscriptParts[]
   try {
     transcriptParts = getTranscriptParts(feature)
   } catch {

package/test_data/gene.json

@@ -90,8 +90,8 @@
               "id": "abc",
               "refSeq": "chr1",
               "type": "CDS_region",
-              "min": "1350",
-              "max": "1400",
+              "min": 1350,
+              "max": 1400,
               "strand": 1,
               "attributes": {
                 "gff_id": ["cds_region10001"]