jbrowse-plugin-msaview 2.3.8 → 2.4.0

package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts

@@ -1,3 +1,10 @@
 export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'
+
 export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'] as const
 export type MsaAlgorithm = (typeof msaAlgorithms)[number]
+
+export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'] as const
+export type BlastDatabase = (typeof blastDatabaseOptions)[number]
+
+export const blastPrograms = ['blastp', 'quick-blastp'] as const
+export type BlastProgram = (typeof blastPrograms)[number]

package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -1,6 +1,5 @@
 import React, { useState } from 'react'
 
-import { readConfObject } from '@jbrowse/core/configuration'
 import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui'
 import { getContainingView, getEnv, getSession } from '@jbrowse/core/util'
 import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material'
@@ -15,8 +14,8 @@ import { useTranscriptSelection } from '../useTranscriptSelection'
 import { swrFlags } from './consts'
 import { fetchMSA, fetchMSAList } from './fetchMSAData'
 import { preCalculatedLaunchView } from './preCalculatedLaunchView'
+import { readMsaDatasets } from './types'
 
-import type { Dataset } from './types'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -45,10 +44,7 @@ const PreLoadedMSA = observer(function ({
   const { assemblyNames } = view
   const [viewError, setViewError] = useState<unknown>()
 
-  const { jbrowse } = session
-  const datasets = readConfObject(jbrowse, ['msa', 'datasets']) as
-    | Dataset[]
-    | undefined
+  const datasets = readMsaDatasets(session.jbrowse)
   const [selectedDatasetId, setSelectedDatasetId] = useState(
     datasets?.[0]?.datasetId,
   )
@@ -58,14 +54,8 @@ const PreLoadedMSA = observer(function ({
     isLoading: msaListLoading,
     error: msaListFetchError,
   } = useSWR(
-    selectedDatasetId ? `${selectedDatasetId}-msa-list` : 'none-msa-list',
-    () =>
-      selectedDataset
-        ? fetchMSAList({
-            config: selectedDataset.adapter,
-            pluginManager,
-          })
-        : undefined,
+    selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null,
+    () => fetchMSAList({ config: selectedDataset!.adapter, pluginManager }),
     swrFlags,
   )
 
@@ -83,25 +73,20 @@ const PreLoadedMSA = observer(function ({
     isLoading: msaDataLoading,
     error: msaDataFetchError,
   } = useSWR(
-    selectedId && selectedDatasetId
-      ? `${selectedDatasetId}-${selectedId}-${msaList?.length}-msa`
-      : 'none-msa',
+    selectedId && selectedDataset && msaList
+      ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
+      : null,
     () =>
-      selectedId && selectedDataset && msaList
-        ? fetchMSA({
-            msaId: selectedId,
-            config: selectedDataset.adapter,
-            pluginManager,
-          })
-        : undefined,
+      fetchMSA({
+        msaId: selectedId,
+        config: selectedDataset!.adapter,
+        pluginManager,
+      }),
     swrFlags,
   )
 
   const e =
     msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError
-  if (e) {
-    console.error(e)
-  }
   return (
     <>
       <DialogContent className={classes.dialogContent}>

package/src/LaunchMsaView/components/PreLoadedMSA/types.ts

@@ -1,3 +1,5 @@
+import { readConfObject } from '@jbrowse/core/configuration'
+
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
 export interface Dataset {
@@ -6,3 +8,7 @@ export interface Dataset {
   description?: string
   adapter: AnyConfigurationModel
 }
+
+export function readMsaDatasets(jbrowse: AnyConfigurationModel) {
+  return readConfObject(jbrowse, ['msa', 'datasets']) as Dataset[] | undefined
+}

package/src/LaunchMsaView/components/types.ts

@@ -6,7 +6,4 @@ export interface Feat {
 
 export interface SeqState {
   seq: string
-  upstream?: string
-  downstream?: string
-  error?: unknown
 }

package/src/LaunchMsaView/components/useFeatureSequence.ts

@@ -6,23 +6,17 @@ import type { Feature } from '@jbrowse/core/util'
 export function useFeatureSequence({
   view,
   feature,
-  upDownBp = 0,
-  forceLoad = true,
 }: {
   view: { assemblyNames?: string[] } | undefined
   feature?: Feature
-  upDownBp?: number
-  forceLoad?: boolean
 }) {
   const { sequence, error } = useSWRFeatureSequence({
     view,
     feature,
-    upDownBp,
-    forceLoad,
   })
 
   const proteinSequence =
-    sequence && !('error' in sequence) && feature
+    sequence && feature
       ? getProteinSequenceFromFeature({
           seq: sequence.seq,
           feature,

package/src/LaunchMsaView/components/useSWRFeatureSequence.ts

@@ -3,77 +3,50 @@ import useSWR from 'swr'
 
 import { fetchSeq } from './fetchSeq'
 
-import type { SeqState } from './types'
 import type { Feature } from '@jbrowse/core/util'
 
 async function featureSequenceFetcher({
   feature,
   assemblyName,
-  upDownBp,
   view,
 }: {
   feature: Feature
   assemblyName: string
-  upDownBp: number
   view: { assemblyNames?: string[] }
-}): Promise<SeqState | undefined> {
+}) {
   const session = getSession(view)
   const { start, end, refName } = feature.toJSON() as {
     start: number
     end: number
     refName: string
   }
-
-  const b = start - upDownBp
-  const e = end + upDownBp
-  const [seq, upstream, downstream] = await Promise.all([
-    fetchSeq({
-      start,
-      end,
-      refName,
-      assemblyName,
-      session,
-    }),
-    fetchSeq({
-      start: Math.max(0, b),
-      end: start,
-      refName,
-      assemblyName,
-      session,
-    }),
-    fetchSeq({
-      start: end,
-      end: e,
-      refName,
-      assemblyName,
-      session,
-    }),
-  ])
-  return { seq, upstream, downstream }
+  const seq = await fetchSeq({
+    start,
+    end,
+    refName,
+    assemblyName,
+    session,
+  })
+  return { seq }
 }
 
 export function useSWRFeatureSequence({
   view,
   feature,
-  upDownBp = 0,
-  forceLoad = true,
 }: {
   view: { assemblyNames?: string[] } | undefined
   feature?: Feature
-  upDownBp?: number
-  forceLoad?: boolean
 }) {
   const assemblyName = view?.assemblyNames?.[0]
   const { data, error } = useSWR(
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     feature && assemblyName && view
-      ? [feature.id(), assemblyName, upDownBp, forceLoad, 'feature-sequence']
+      ? [feature.id(), assemblyName, 'feature-sequence']
       : null,
     () =>
       featureSequenceFetcher({
         feature: feature!,
         assemblyName: assemblyName!,
-        upDownBp,
         view: view!,
       }),
     {

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -8,7 +8,10 @@ import {
   retrieveMsaData,
   storeMsaData,
 } from './msaDataStore'
-import { gappedToUngappedPosition, isProteinView } from './structureConnection'
+import {
+  gappedToUngappedPosition,
+  getProteinViews,
+} from './structureConnection'
 import { getUniprotIdFromAlphaFoldUrl } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
@@ -41,8 +44,7 @@ export function loadStoredData(self: JBrowsePluginMsaViewModel) {
 export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
   const { rows, dataStoreId } = self
   if (rows.length > 0 && !dataStoreId) {
-    const hasFilehandle = !!(self.msaFilehandle ?? self.treeFilehandle)
-    if (hasFilehandle) {
+    if (self.msaFilehandle || self.treeFilehandle) {
       return
     }
 
@@ -194,18 +196,13 @@ export function highlightConnectedStructures(self: JBrowsePluginMsaViewModel) {
 }
 
 export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
-  const views = getSession(self).views as unknown[]
   const { connectedViewId, uniprotId, rows, connectedStructures } = self
 
   if (!uniprotId || rows.length === 0) {
     return
   }
 
-  for (const view of views) {
-    if (!isProteinView(view)) {
-      continue
-    }
-
+  for (const view of getProteinViews(getSession(self).views)) {
     for (
       let structureIdx = 0;
       structureIdx < view.structures.length;
@@ -245,7 +242,6 @@ export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
 }
 
 export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
-  const views = getSession(self).views as unknown[]
   const { connectedViewId, transcriptToMsaMap, querySeqName } = self
 
   if (!connectedViewId || !transcriptToMsaMap) {
@@ -254,11 +250,7 @@ export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
 
   const columns = new Set<number>()
 
-  for (const view of views) {
-    if (!isProteinView(view)) {
-      continue
-    }
-
+  for (const view of getProteinViews(getSession(self).views)) {
     for (const structure of view.structures) {
       if (structure.connectedViewId !== connectedViewId) {
         continue

package/src/MsaViewPanel/components/ConnectStructureDialog.tsx

@@ -15,7 +15,7 @@ import {
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import { isProteinView } from '../structureConnection'
+import { getProteinViews } from '../structureConnection'
 
 import type { JBrowsePluginMsaViewModel } from '../model'
 
@@ -39,7 +39,7 @@ const ConnectStructureDialog = observer(function ConnectStructureDialog({
   const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName)
   const [error, setError] = useState<string>()
 
-  const proteinViews = (session.views as unknown[]).filter(isProteinView)
+  const proteinViews = getProteinViews(session.views)
 
   const selectedView = proteinViews.find(v => v.id === selectedViewId)
   const structures = selectedView?.structures ?? []

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -60,7 +60,7 @@ const LoadingBLAST = observer(function LoadingBLAST2({
   model: JBrowsePluginMsaViewModel
   baseUrl: string
 }) {
-  const { progress, rid, error, processing } = model
+  const { progress, rid, error } = model
   const { classes } = useStyles()
   return (
     <div className={classes.margin}>
@@ -69,8 +69,9 @@ const LoadingBLAST = observer(function LoadingBLAST2({
         <RIDError baseUrl={baseUrl} rid={rid} error={error} />
       ) : rid ? (
         <RIDProgress baseUrl={baseUrl} rid={rid} progress={progress} />
-      ) : null}
-      <Typography>{processing || 'Initializing BLAST query'}</Typography>
+      ) : (
+        <Typography>{progress || 'Initializing BLAST query'}</Typography>
+      )}
     </div>
   )
 })

package/src/MsaViewPanel/model.ts

@@ -22,13 +22,17 @@ import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment'
 import {
-  isProteinView,
-  mapToRecord,
+  getProteinViews,
   ungappedToGappedPosition,
 } from './structureConnection'
 
 import type { ProteinView, StructureConnection } from './structureConnection'
 import type { MafRegion, MsaViewInitState } from './types'
+import type {
+  BlastDatabase,
+  BlastProgram,
+  MsaAlgorithm,
+} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
 import type { Feature } from '@jbrowse/core/util'
 import type { Instance } from '@jbrowse/mobx-state-tree'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -49,9 +53,9 @@ export interface IRegion {
 
 export interface BlastParams {
   baseUrl: string
-  blastDatabase: string
-  msaAlgorithm: string
-  blastProgram: string
+  blastDatabase: BlastDatabase
+  msaAlgorithm: MsaAlgorithm
+  blastProgram: BlastProgram
   selectedTranscript?: Feature
   proteinSequence: string
   rid?: string
@@ -179,13 +183,6 @@ export default function stateModelFactory() {
           : undefined
       },
 
-      /**
-       * #getter
-       */
-      get processing() {
-        return !!self.progress
-      },
-
       /**
        * #getter
        */
@@ -198,14 +195,12 @@ export default function stateModelFactory() {
        * #getter
        */
       get connectedProteinViews() {
-        const { views } = getSession(self)
-        const unknownViews = views as unknown[]
+        const proteinViews = getProteinViews(getSession(self).views)
         const result: (StructureConnection & { proteinView: ProteinView })[] =
           []
         for (const conn of self.connectedStructures) {
-          const proteinView = unknownViews.find(
-            (v): v is ProteinView =>
-              isProteinView(v) && v.id === conn.proteinViewId,
+          const proteinView = proteinViews.find(
+            v => v.id === conn.proteinViewId,
           )
           if (proteinView) {
             result.push({ ...conn, proteinView })
@@ -251,12 +246,6 @@ export default function stateModelFactory() {
         }
         return genomeToMSA({ model: self as JBrowsePluginMsaViewModel })
       },
-      /**
-       * #getter
-       */
-      get clickCol2() {
-        return undefined
-      },
     }))
 
     .actions(self => ({
@@ -383,10 +372,8 @@ export default function stateModelFactory() {
 
         const ungappedMsaSequence = msaSequence.replaceAll('-', '')
 
-        const { views } = getSession(self)
-
-        const proteinView = (views as unknown[]).find(
-          (v): v is ProteinView => isProteinView(v) && v.id === proteinViewId,
+        const proteinView = getProteinViews(getSession(self).views).find(
+          v => v.id === proteinViewId,
         )
         if (!proteinView) {
           throw new Error(`ProteinView "${proteinViewId}" not found`)
@@ -412,8 +399,8 @@ export default function stateModelFactory() {
           proteinViewId,
           structureIdx,
           msaRowName: rowName,
-          msaToStructure: mapToRecord(seq1ToSeq2),
-          structureToMsa: mapToRecord(seq2ToSeq1),
+          msaToStructure: Object.fromEntries(seq1ToSeq2),
+          structureToMsa: Object.fromEntries(seq2ToSeq1),
         }
 
         self.connectedStructures.push(connection)

package/src/MsaViewPanel/msaDataStore.ts

@@ -66,15 +66,6 @@ export async function retrieveMsaData(id: string) {
   }
 }
 
-export async function deleteMsaData(id: string) {
-  try {
-    const db = await getDB()
-    await db.delete(STORE_NAME, id)
-  } catch (e) {
-    console.warn('Failed to delete MSA data:', e)
-  }
-}
-
 export async function cleanupOldData(maxAgeMs = 7 * 24 * 60 * 60 * 1000) {
   try {
     const db = await getDB()

package/src/MsaViewPanel/structureConnection.test.ts

@@ -2,7 +2,6 @@ import { describe, expect, test } from 'vitest'
 
 import {
   gappedToUngappedPosition,
-  mapToRecord,
   ungappedToGappedPosition,
 } from './structureConnection'
 
@@ -121,23 +120,3 @@ describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', (
     }
   })
 })
-
-describe('mapToRecord', () => {
-  test('converts Map to Record', () => {
-    const map = new Map<number, number>([
-      [0, 5],
-      [1, 10],
-      [2, 15],
-    ])
-    const record = mapToRecord(map)
-    expect(record[0]).toBe(5)
-    expect(record[1]).toBe(10)
-    expect(record[2]).toBe(15)
-  })
-
-  test('handles empty Map', () => {
-    const map = new Map<number, number>()
-    const record = mapToRecord(map)
-    expect(Object.keys(record)).toHaveLength(0)
-  })
-})

package/src/MsaViewPanel/structureConnection.ts

@@ -21,6 +21,13 @@ export function isProteinView(view: unknown): view is ProteinView {
   return v.type === 'ProteinView' && Array.isArray(v.structures)
 }
 
+/**
+ * Extract all ProteinView instances from a session's views array.
+ */
+export function getProteinViews(views: { type: string }[]): ProteinView[] {
+  return (views as unknown[]).filter(isProteinView)
+}
+
 /**
  * Represents a connection between the MSA view and a protein structure
  */
@@ -82,10 +89,3 @@ export function ungappedToGappedPosition(
   }
   return undefined
 }
-
-/**
- * Convert Map to plain object for MST frozen storage
- */
-export function mapToRecord(map: Map<number, number>): Record<number, number> {
-  return Object.fromEntries(map)
-}

package/src/utils/blastCache.ts

@@ -1,5 +1,11 @@
 import { openDB } from 'idb'
 
+import type {
+  BlastDatabase,
+  BlastProgram,
+  MsaAlgorithm,
+} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+
 const DB_NAME = 'jbrowse-msaview-blast-cache'
 const STORE_NAME = 'blast-results'
 const DB_VERSION = 2
@@ -7,9 +13,9 @@ const DB_VERSION = 2
 export interface CachedBlastResult {
   id: string
   proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  msaAlgorithm: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
+  msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
   treeMetadata: string
@@ -36,8 +42,8 @@ async function getDB() {
 
 function createCacheKey(
   proteinSequence: string,
-  blastDatabase: string,
-  blastProgram: string,
+  blastDatabase: BlastDatabase,
+  blastProgram: BlastProgram,
   transcriptId?: string,
 ) {
   if (transcriptId) {
@@ -46,27 +52,6 @@ function createCacheKey(
   return `${blastDatabase}:${blastProgram}:${proteinSequence}`
 }
 
-export async function getCachedBlastResult({
-  proteinSequence,
-  blastDatabase,
-  blastProgram,
-  transcriptId,
-}: {
-  proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  transcriptId?: string
-}) {
-  const db = await getDB()
-  const id = createCacheKey(
-    proteinSequence,
-    blastDatabase,
-    blastProgram,
-    transcriptId,
-  )
-  return db.get(STORE_NAME, id)
-}
-
 export async function saveBlastResult({
   proteinSequence,
   blastDatabase,
@@ -82,9 +67,9 @@ export async function saveBlastResult({
   geneName,
 }: {
   proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  msaAlgorithm: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
+  msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
   treeMetadata: string
@@ -127,14 +112,6 @@ export async function getAllCachedResults() {
   return results.toSorted((a, b) => b.timestamp - a.timestamp)
 }
 
-export async function getCachedResultsByGeneId(geneId: string) {
-  const db = await getDB()
-  const results = await db.getAll(STORE_NAME)
-  return results
-    .filter(r => r.geneId === geneId)
-    .toSorted((a, b) => b.timestamp - a.timestamp)
-}
-
 export async function deleteCachedResult(id: string) {
   const db = await getDB()
   await db.delete(STORE_NAME, id)

package/src/utils/msa.ts

@@ -1,9 +1,11 @@
 import { textfetch, timeout } from './fetch'
 
+import type { MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+
 const base = `https://www.ebi.ac.uk/Tools/services/rest`
 
 const algorithms: Record<
-  string,
+  MsaAlgorithm,
   {
     params: Record<string, string>
     msaResult: string
@@ -38,7 +40,7 @@ async function wait({
   algorithm,
 }: {
   jobId: string
-  algorithm: string
+  algorithm: MsaAlgorithm
   onProgress: (arg: string) => void
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
@@ -62,14 +64,11 @@ export async function launchMSA({
   sequence,
   onProgress,
 }: {
-  algorithm: string
+  algorithm: MsaAlgorithm
   sequence: string
   onProgress: (arg: string) => void
 }) {
   const config = algorithms[algorithm]
-  if (!config) {
-    throw new Error(`unknown algorithm: ${algorithm}`)
-  }
 
   onProgress(`Launching ${algorithm} MSA...`)
 

package/src/utils/ncbiBlast.ts

@@ -1,6 +1,10 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
 
 import type { BlastResults } from './types'
+import type {
+  BlastDatabase,
+  BlastProgram,
+} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
 
 export async function queryBlastFromRid({
   rid,
@@ -35,8 +39,8 @@ export async function queryBlast({
   onRid,
 }: {
   query: string
-  blastDatabase: string
-  blastProgram: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
   baseUrl: string
   onProgress: (arg: string) => void
   onRid: (arg: string) => void
@@ -59,8 +63,8 @@ async function initialQuery({
   baseUrl,
 }: {
   query: string
-  blastProgram: string
-  blastDatabase: string
+  blastProgram: BlastProgram
+  blastDatabase: BlastDatabase
   baseUrl: string
 }) {
   const res = await textfetch(baseUrl, {
@@ -70,7 +74,7 @@ async function initialQuery({
       PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
       DATABASE: blastDatabase,
       QUERY: query,
-      ...(blastDatabase === 'nr_clustered_seq'
+      ...(blastDatabase === 'nr_cluster_seq'
         ? {
             CLUSTERED_DB: 'on',
             DB_TYPE: 'Experimental Databases',