jbrowse-plugin-msaview 2.4.2 → 2.4.4

package/src/LaunchMsaView/components/useTranscriptSelection.ts

@@ -5,26 +5,24 @@ import { useFeatureSequence } from './useFeatureSequence'
 
 import type { Feature } from '@jbrowse/core/util'
 
-function featureInValidIds(feature: Feature, validIds: string[]): boolean {
-  return validIds.some(id => featureMatchesId(feature, id))
-}
-
 function findValidSelection(
   currentId: string,
   options: Feature[],
   validIds: string[] | undefined,
 ): string | undefined {
-  if (!validIds || validIds.length === 0) {
-    return undefined
+  if (validIds && validIds.length > 0) {
+    const currentFeature = options.find(opt => getId(opt) === currentId)
+    const currentIsValid =
+      currentFeature &&
+      validIds.some(id => featureMatchesId(currentFeature, id))
+    if (currentFeature && !currentIsValid) {
+      const validOption = options.find(opt =>
+        validIds.some(id => featureMatchesId(opt, id)),
+      )
+      return validOption ? getId(validOption) : undefined
+    }
   }
-
-  const currentFeature = options.find(opt => getId(opt) === currentId)
-  if (!currentFeature || featureInValidIds(currentFeature, validIds)) {
-    return undefined
-  }
-
-  const validOption = options.find(opt => featureInValidIds(opt, validIds))
-  return validOption ? getId(validOption) : undefined
+  return undefined
 }
 
 export function useTranscriptSelection({
@@ -39,7 +37,7 @@ export function useTranscriptSelection({
   const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature])
   const [selectedId, setSelectedId] = useState(() => getId(options[0]))
   const validatedSelectedId =
-    findValidSelection(selectedId, options, validIds) || selectedId
+    findValidSelection(selectedId, options, validIds) ?? selectedId
   const selectedTranscript = options.find(
     val => getId(val) === validatedSelectedId,
   )

package/src/LaunchMsaView/util.ts

@@ -1,6 +1,19 @@
-import { sum } from '@jbrowse/core/util'
+import { getContainingView, sum } from '@jbrowse/core/util'
 
-import type { Feature } from '@jbrowse/core/util'
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+export function getLinearGenomeView(model: AbstractTrackModel) {
+  return getContainingView(model) as LinearGenomeViewModel
+}
+
+function uniqueDefined(vals: (string | undefined)[]): string[] {
+  return [...new Set(vals.filter((v): v is string => !!v))]
+}
+
+function joinDefined(sep: string, parts: (string | undefined)[]): string {
+  return parts.filter((p): p is string => !!p).join(sep)
+}
 
 export function getTranscriptFeatures(feature: Feature) {
   // check if we are looking at a 'two-level' or 'three-level' feature by
@@ -42,16 +55,14 @@ export function getId(val?: Feature): string {
 }
 
 export function getMatchableIds(val?: Feature): string[] {
-  if (!val) {
-    return []
-  }
-  const ids = [
-    val.id(),
-    val.get('name'),
-    val.get('id'),
-    val.get('transcript_id'),
-  ].filter((id): id is string => !!id)
-  return [...new Set(ids)]
+  return val
+    ? uniqueDefined([
+        val.id(),
+        val.get('name'),
+        val.get('id'),
+        val.get('transcript_id'),
+      ])
+    : []
 }
 
 export function featureMatchesId(feature: Feature, id: string): boolean {
@@ -59,20 +70,20 @@ export function featureMatchesId(feature: Feature, id: string): boolean {
 }
 
 export function getTranscriptDisplayName(val?: Feature) {
-  return val === undefined
-    ? ''
-    : [val.get('name'), val.get('id')].filter(f => !!f).join(' ')
+  return val ? joinDefined(' ', [val.get('name'), val.get('id')]) : ''
 }
 
 export function getGeneDisplayName(val?: Feature) {
-  return val === undefined
-    ? ''
-    : [
+  return val
+    ? joinDefined(' ', [
         val.get('gene_name') ?? val.get('name'),
-        val.get('id') ? `(${val.get('id')})` : '',
-      ]
-        .filter(f => !!f)
-        .join(' ')
+        val.get('id') ? `(${val.get('id')})` : undefined,
+      ])
+    : ''
+}
+
+export function getBlastViewTitle(feature: Feature, transcript: Feature) {
+  return `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(transcript)}`
 }
 
 export function getSortedTranscriptFeatures(feature: Feature) {
@@ -87,12 +98,11 @@ export function cleanProteinSequence(seq: string) {
 }
 
 export function getGeneIdentifiers(feature: Feature): string[] {
-  const ids = [
+  return uniqueDefined([
     feature.id(),
     feature.get('id'),
     feature.get('name'),
     feature.get('gene_id'),
     feature.get('gene_name'),
-  ].filter((id): id is string => !!id)
-  return [...new Set(ids)]
+  ])
 }

package/src/MsaViewPanel/util.ts

@@ -14,9 +14,9 @@ export function checkHovered(hovered: unknown): hovered is {
 }
 
 interface AssemblyManagerLike {
-  get: (name: string) =>
-    | { getCanonicalRefName: (r: string) => string | undefined }
-    | undefined
+  get: (
+    name: string,
+  ) => { getCanonicalRefName: (r: string) => string | undefined } | undefined
 }
 
 export function getCanonicalRefName({

package/src/{LaunchMsaView/components/PreLoadedMSA/consts.ts → utils/swrConfig.ts}

@@ -1,4 +1,4 @@
-export const swrFlags = {
+export const staticSwrConfig = {
   revalidateOnFocus: false,
   revalidateOnReconnect: false,
   revalidateIfStale: false,

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.4.2'
+export const version = '2.4.4'

package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;IACtB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA"}