@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.6

package/src/util/annotationFeatureUtils.ts

@@ -0,0 +1,53 @@
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+
+export function getFeatureName(feature: AnnotationFeature) {
+  const { attributes } = feature
+  const name = attributes.get('gff_name')
+  if (name) {
+    return name[0]
+  }
+  return ''
+}
+
+export function getFeatureId(feature: AnnotationFeature) {
+  const { attributes } = feature
+  const id = attributes.get('gff_id')
+  const transcript_id = attributes.get('transcript_id')
+  const exon_id = attributes.get('exon_id')
+  const protein_id = attributes.get('protein_id')
+  if (id) {
+    return id[0]
+  }
+  if (transcript_id) {
+    return transcript_id[0]
+  }
+  if (exon_id) {
+    return exon_id[0]
+  }
+  if (protein_id) {
+    return protein_id[0]
+  }
+  return ''
+}
+
+export function getFeatureNameOrId(feature: AnnotationFeature) {
+  const name = getFeatureName(feature)
+  const id = getFeatureId(feature)
+  if (name) {
+    return `: ${name}`
+  }
+  if (id) {
+    return `: ${id}`
+  }
+  return ''
+}
+
+export function getStrand(strand: number | undefined) {
+  if (strand === 1) {
+    return 'Forward'
+  }
+  if (strand === -1) {
+    return 'Reverse'
+  }
+  return ''
+}

package/src/util/index.ts

@@ -1,8 +1,8 @@
 import { getParent } from 'mobx-state-tree'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 
 export async function createFetchErrorMessage(
   response: Response,
@@ -29,3 +29,4 @@ export function getApolloInternetAccount(session: ApolloSessionModel) {
 }
 
 export * from './loadAssemblyIntoClient'
+export * from './annotationFeatureUtils'

package/src/util/loadAssemblyIntoClient.ts

@@ -1,7 +1,14 @@
-import { ClientDataStore, checkRegistry } from '@apollo-annotation/common'
-import { ApolloAssemblyI, CheckResultSnapshot } from '@apollo-annotation/mst'
+import { type ClientDataStore, checkRegistry } from '@apollo-annotation/common'
+import {
+  type ApolloAssemblyI,
+  type CheckResultSnapshot,
+} from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
-import gff, { GFF3Comment, GFF3Feature, GFF3Sequence } from '@gmod/gff'
+import gff, {
+  type GFF3Comment,
+  type GFF3Feature,
+  type GFF3Sequence,
+} from '@gmod/gff'
 import { getSnapshot } from 'mobx-state-tree'
 
 export async function loadAssemblyIntoClient(

package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx

@@ -1,13 +0,0 @@
-/* eslint-disable @typescript-eslint/require-await */
-import { RenderProps, RendererType } from '@jbrowse/core/pluggableElementTypes'
-import RpcManager from '@jbrowse/core/rpc/RpcManager'
-
-export default class ApolloSixFrameRenderer extends RendererType {
-  async renderInClient(_rpcManager: RpcManager, args: RenderProps) {
-    return this.render(args)
-  }
-
-  async freeResourcesInClient(_rpcManager: RpcManager, _args: RenderProps) {
-    return 0
-  }
-}