Implements issue #325

GMOD · Nov 20, 2023 · cf300c3 · cf300c3
1 parent 2243bbb
commit cf300c3
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Showing 2 changed files with 35 additions and 9 deletions.
diff --git a/packages/jbrowse-plugin-apollo/src/index.ts b/packages/jbrowse-plugin-apollo/src/index.ts
@@ -18,8 +18,9 @@ import {
 } from '@jbrowse/core/util'
 import { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
-import { changeRegistry } from 'apollo-common'
+import { changeRegistry, checkRegistry } from 'apollo-common'
 import {
+  CDSCheck,
   CoreValidation,
   ParentChildValidation,
   changes,
@@ -91,6 +92,9 @@ for (const [changeName, change] of Object.entries(changes)) {
   changeRegistry.registerChange(changeName, change)
 }
 
+const cdsCheck = new CDSCheck()
+checkRegistry.registerCheck(cdsCheck.name, cdsCheck)
+
 validationRegistry.registerValidation(new CoreValidation())
 validationRegistry.registerValidation(new ParentChildValidation())
 

diff --git a/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts b/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts
@@ -1,6 +1,11 @@
 import gff, { GFF3Comment, GFF3Feature, GFF3Sequence } from '@gmod/gff'
-import { ClientDataStore } from 'apollo-common'
-import { AnnotationFeatureSnapshot, CheckResultSnapshot } from 'apollo-mst'
+import { ClientDataStore, checkRegistry } from 'apollo-common'
+import {
+  AnnotationFeatureSnapshot,
+  ApolloAssemblyI,
+  CheckResultSnapshot,
+} from 'apollo-mst'
+import { getSnapshot } from 'mobx-state-tree'
 import { nanoid } from 'nanoid'
 
 export async function loadAssemblyIntoClient(
@@ -25,16 +30,14 @@ export async function loadAssemblyIntoClient(
     assembly = apolloDataStore.addAssembly(assemblyId)
   }
 
-  const checkResults: CheckResultSnapshot[] = []
   for (const seqLine of featuresAndSequences) {
     if (Array.isArray(seqLine)) {
       // regular feature
       const feature = createFeature(seqLine)
 
-      let ref = assembly.refSeqs.get(feature.refSeq)
-      if (!ref) {
-        ref = assembly.addRefSeq(feature.refSeq, feature.refSeq)
-      }
+      const ref =
+        assembly.refSeqs.get(feature.refSeq) ??
+        assembly.addRefSeq(feature.refSeq, feature.refSeq)
       if (!ref.features.has(feature._id)) {
         ref.addFeature(feature)
       }
@@ -57,15 +60,34 @@ export async function loadAssemblyIntoClient(
       })
     }
   }
-  apolloDataStore.addCheckResults(checkResults)
 
   if (sequenceFeatureCount === 0) {
     throw new Error('No embedded FASTA section found in GFF3')
   }
 
+  const checkResults: CheckResultSnapshot[] = await checkFeatures(assembly)
+  apolloDataStore.addCheckResults(checkResults)
   return assembly
 }
 
+async function checkFeatures(
+  assembly: ApolloAssemblyI,
+): Promise<CheckResultSnapshot[]> {
+  let checkResults: CheckResultSnapshot[] = []
+  for (const ref of assembly.refSeqs.values()) {
+    for (const feature of ref.features.values()) {
+      for (const check of checkRegistry.getChecks().values()) {
+        const result: CheckResultSnapshot[] = await check.checkFeature(
+          getSnapshot(feature),
+          async (start: number, stop: number) => ref.getSequence(start, stop),
+        );
+        checkResults = [...checkResults, ...result]
+      }
+    }
+  }
+  return checkResults
+}
+
 function createFeature(gff3Feature: GFF3Feature): AnnotationFeatureSnapshot {
   const [firstFeature] = gff3Feature
   const {