@apollo-annotation/mst 0.3.5 → 0.3.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.5",
+  "version": "0.3.6",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"

package/src/AnnotationFeatureModel.ts

@@ -1,10 +1,10 @@
 import { getSession, intersection2 } from '@jbrowse/core/util'
 import {
-  IAnyModelType,
-  IMSTMap,
-  Instance,
-  SnapshotIn,
-  SnapshotOrInstance,
+  type IAnyModelType,
+  type IMSTMap,
+  type Instance,
+  type SnapshotIn,
+  type SnapshotOrInstance,
   cast,
   getParentOfType,
   getSnapshot,
@@ -291,6 +291,48 @@ export const AnnotationFeatureModel = types
         transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'),
       )
     },
+    get looksLikeGene(): boolean {
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const { apolloDataStore } = session
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      if (!featureTypeOntology) {
+        return false
+      }
+      const children = self.children as Children
+      if (!children?.size) {
+        return false
+      }
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const isGene =
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        featureTypeOntology.isTypeOf(self.type, 'gene') ||
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        featureTypeOntology.isTypeOf(self.type, 'pseudogene')
+      if (!isGene) {
+        return false
+      }
+      for (const [, child] of children) {
+        if (
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+        ) {
+          const { children: grandChildren } = child
+          if (!grandChildren?.size) {
+            return false
+          }
+          return [...grandChildren.values()].some((grandchild) =>
+            // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+            featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
+          )
+        }
+      }
+      return false
+    },
   }))
   .actions((self) => ({
     setAttributes(attributes: Map<string, string[]>) {

package/src/ApolloAssembly.ts

@@ -1,4 +1,4 @@
-import { Instance, SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
 
 import { ApolloRefSeq } from './ApolloRefSeq'
 

package/src/ApolloRefSeq.ts

@@ -1,14 +1,14 @@
 import { isContainedWithin } from '@jbrowse/core/util'
 import {
-  Instance,
-  SnapshotIn,
-  SnapshotOrInstance,
+  type Instance,
+  type SnapshotIn,
+  type SnapshotOrInstance,
   types,
 } from 'mobx-state-tree'
 
 import {
   AnnotationFeatureModel,
-  AnnotationFeatureSnapshot,
+  type AnnotationFeatureSnapshot,
 } from './AnnotationFeatureModel'
 
 export const Sequence = types.model({

package/src/CheckResult.ts

@@ -1,4 +1,4 @@
-import { Instance, SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
 
 import { AnnotationFeatureModel } from './AnnotationFeatureModel'