@apollo-annotation/mst 0.3.5 → 0.3.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.5",
+  "version": "0.3.7",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"

package/src/AnnotationFeatureModel.ts

@@ -1,10 +1,13 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
 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,
@@ -127,14 +130,14 @@ export const AnnotationFeatureModel = types
       return false
     },
     get transcriptExonParts(): TranscriptParts {
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      // eslint-disable-next-line @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
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
-      if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
+      if (
+        !featureTypeOntology.isTypeOf(self.type, 'transcript') &&
+        !featureTypeOntology.isTypeOf(self.type, 'pseudogenic_transcript')
+      ) {
         throw new Error(
           'Feature is not a transcript or equivalent, cannot calculate exon locations',
         )
@@ -144,7 +147,6 @@ export const AnnotationFeatureModel = types
         throw new Error('No exons in transcript')
       }
       const sortedChildren = [...children.values()]
-        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
         .filter((child) => featureTypeOntology.isTypeOf(child.type, 'exon'))
         .sort((a, b) => a.min - b.min)
       let lastMax = self.min
@@ -177,14 +179,14 @@ export const AnnotationFeatureModel = types
       return parts
     },
     get transcriptParts(): TranscriptParts[] {
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      // eslint-disable-next-line @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
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
-      if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
+      if (
+        !featureTypeOntology.isTypeOf(self.type, 'transcript') &&
+        !featureTypeOntology.isTypeOf(self.type, 'pseudogenic_transcript')
+      ) {
         throw new Error(
           'Only features of type "transcript" or equivalent can calculate CDS locations',
         )
@@ -193,9 +195,8 @@ export const AnnotationFeatureModel = types
       if (!children) {
         throw new Error('no CDS or exons in transcript')
       }
-      const cdsChildren = [...children.values()].filter(
-        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
-        (child) => featureTypeOntology.isTypeOf(child.type, 'CDS'),
+      const cdsChildren = [...children.values()].filter((child) =>
+        featureTypeOntology.isTypeOf(child.type, 'CDS'),
       )
       const transcriptParts: TranscriptParts[] = []
       if (cdsChildren.length === 0) {
@@ -208,7 +209,6 @@ export const AnnotationFeatureModel = types
         let hasIntersected = false
         const exonLocations: TranscriptPartLocation[] = []
         for (const [, child] of children) {
-          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
           if (featureTypeOntology.isTypeOf(child.type, 'exon')) {
             exonLocations.push({ min: child.min, max: child.max })
           }
@@ -291,6 +291,40 @@ export const AnnotationFeatureModel = types
         transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'),
       )
     },
+    get looksLikeGene(): boolean {
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      const { apolloDataStore } = session
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      if (!featureTypeOntology) {
+        return false
+      }
+      const children = self.children as Children
+      if (!children?.size) {
+        return false
+      }
+      const isGene =
+        featureTypeOntology.isTypeOf(self.type, 'gene') ||
+        featureTypeOntology.isTypeOf(self.type, 'pseudogene')
+      if (!isGene) {
+        return false
+      }
+      for (const [, child] of children) {
+        if (
+          featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+          featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+        ) {
+          const { children: grandChildren } = child
+          if (!grandChildren?.size) {
+            return false
+          }
+          return [...grandChildren.values()].some((grandchild) =>
+            featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
+          )
+        }
+      }
+      return false
+    },
   }))
   .actions((self) => ({
     setAttributes(attributes: Map<string, string[]>) {
@@ -310,7 +344,7 @@ export const AnnotationFeatureModel = types
     },
     setMin(min: number) {
       if (min > self.max) {
-        throw new Error(`Min "${min}" is greater than max "${self.max}"`)
+        throw new Error(`Min "${min + 1}" is greater than max "${self.max}"`)
       }
       if (self.min !== min) {
         self.min = min

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 +1,15 @@
-import { isContainedWithin } from '@jbrowse/core/util'
+import { doesIntersect2, isContainedWithin } from '@jbrowse/core/util'
 import {
-  Instance,
-  SnapshotIn,
-  SnapshotOrInstance,
+  type Instance,
+  type SnapshotIn,
+  type SnapshotOrInstance,
   types,
 } from 'mobx-state-tree'
 
 import {
+  type AnnotationFeature,
   AnnotationFeatureModel,
-  AnnotationFeatureSnapshot,
+  type AnnotationFeatureSnapshot,
 } from './AnnotationFeatureModel'
 
 export const Sequence = types.model({
@@ -124,6 +125,15 @@ export const ApolloRefSeq = types
       }
       return ''
     },
+    getFeatures(min: number, max: number): AnnotationFeature[] {
+      const features: AnnotationFeature[] = []
+      for (const [, feature] of self.features) {
+        if (doesIntersect2(feature.min, feature.max, min, max)) {
+          features.push(feature)
+        }
+      }
+      return features
+    },
   }))
 
 // eslint disables because of

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'