jbrowse-plugin-msaview 2.2.7 → 2.2.11

package/src/LaunchMsaView/components/TranscriptSelector.tsx

@@ -1,12 +1,12 @@
 import React, { useState } from 'react'
 
 import { Feature } from '@jbrowse/core/util'
-import { Button, MenuItem } from '@mui/material'
+import { Button, MenuItem, TextField } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 
 import ReadOnlyTextField2 from '../../components/ReadOnlyTextField2'
-import TextField2 from '../../components/TextField2'
 import {
+  featureMatchesId,
   getGeneDisplayName,
   getId,
   getTranscriptDisplayName,
@@ -25,6 +25,7 @@ const useStyles = makeStyles()({
 export default function TranscriptSelector({
   feature,
   options,
+  selectedId,
   selectedTranscript,
   onTranscriptChange,
   proteinSequence,
@@ -32,6 +33,7 @@ export default function TranscriptSelector({
 }: {
   feature: Feature
   options: Feature[]
+  selectedId: string
   selectedTranscript: Feature | undefined
   onTranscriptChange: (transcriptId: string) => void
   proteinSequence: string | undefined
@@ -43,18 +45,20 @@ export default function TranscriptSelector({
   return (
     <>
       <div className={classes.flex}>
-        <TextField2
+        <TextField
           variant="outlined"
           label={`Choose isoform of ${getGeneDisplayName(feature)}`}
           select
           className={classes.minWidth}
-          value={getId(selectedTranscript)}
+          value={selectedId}
           onChange={event => {
             onTranscriptChange(event.target.value)
           }}
         >
           {options.map(val => {
-            const inSet = validSet ? validSet.has(getId(val)) : true
+            const inSet = validSet
+              ? [...validSet].some(id => featureMatchesId(val, id))
+              : true
             const { len, mod } = getTranscriptLength(val)
             return (
               <MenuItem value={getId(val)} key={val.id()} disabled={!inSet}>
@@ -64,7 +68,7 @@ export default function TranscriptSelector({
               </MenuItem>
             )
           })}
-        </TextField2>
+        </TextField>
         <div style={{ alignContent: 'center', marginLeft: 20 }}>
           <Button
             variant="contained"

package/src/LaunchMsaView/components/useTranscriptSelection.ts

@@ -1,10 +1,14 @@
 import { useEffect, useMemo, useState } from 'react'
 
-import { getId, getSortedTranscriptFeatures } from '../util'
+import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util'
 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))
+}
+
 export function useTranscriptSelection({
   feature,
   view,
@@ -14,8 +18,8 @@ export function useTranscriptSelection({
   view: { assemblyNames?: string[] } | undefined
   validIds?: string[]
 }) {
-  const options = getSortedTranscriptFeatures(feature)
-  const [selectedId, setSelectedId] = useState(getId(options[0]))
+  const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature])
+  const [selectedId, setSelectedId] = useState(() => getId(options[0]))
   const selectedTranscript = options.find(val => getId(val) === selectedId)
   const { proteinSequence, error } = useFeatureSequence({
     view,
@@ -28,10 +32,15 @@ export function useTranscriptSelection({
   )
 
   useEffect(() => {
-    if (validIds && validIds.length > 0 && !validIds.includes(selectedId)) {
-      const validOption = options.find(opt => validIds.includes(getId(opt)))
-      if (validOption) {
-        setSelectedId(getId(validOption))
+    if (validIds && validIds.length > 0) {
+      const currentFeature = options.find(opt => getId(opt) === selectedId)
+      if (currentFeature && !featureInValidIds(currentFeature, validIds)) {
+        const validOption = options.find(opt =>
+          featureInValidIds(opt, validIds),
+        )
+        if (validOption) {
+          setSelectedId(getId(validOption))
+        }
       }
     }
   }, [validIds, options, selectedId])

package/src/LaunchMsaView/util.ts

@@ -38,7 +38,24 @@ export function getTranscriptLength(feature: Feature) {
   }
 }
 export function getId(val?: Feature): string {
-  return val?.get('name') ?? val?.get('id') ?? ''
+  return val?.id() ?? ''
+}
+
+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)]
+}
+
+export function featureMatchesId(feature: Feature, id: string): boolean {
+  return getMatchableIds(feature).includes(id)
 }
 
 export function getTranscriptDisplayName(val?: Feature) {
@@ -59,7 +76,8 @@ export function getGeneDisplayName(val?: Feature) {
 }
 
 export function getSortedTranscriptFeatures(feature: Feature) {
-  return getTranscriptFeatures(feature).toSorted(
+  const transcripts = getTranscriptFeatures(feature)
+  return transcripts.toSorted(
     (a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len,
   )
 }

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -3,7 +3,7 @@ import { makeId, strip } from '../LaunchMsaView/components/util'
 import { cleanProteinSequence } from '../LaunchMsaView/util'
 import { saveBlastResult } from '../utils/blastCache'
 import { launchMSA } from '../utils/msa'
-import { queryBlast } from '../utils/ncbiBlast'
+import { queryBlast, queryBlastFromRid } from '../utils/ncbiBlast'
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames'
 
 import type { TaxonomyInfo } from '../utils/taxonomyNames'
@@ -21,21 +21,39 @@ export async function doLaunchBlast({
     msaAlgorithm,
     proteinSequence,
     selectedTranscript,
+    rid: existingRid,
   } = self.blastParams!
   const cleanedSeq = cleanProteinSequence(proteinSequence)
 
-  const { hits, rid } = await queryBlast({
-    query: cleanedSeq,
-    blastDatabase,
-    blastProgram,
-    baseUrl,
-    onProgress: arg => {
-      self.setProgress(arg)
-    },
-    onRid: r => {
-      self.setRid(r)
-    },
-  })
+  let hits
+  let rid: string
+  if (existingRid) {
+    self.setRid(existingRid)
+    const result = await queryBlastFromRid({
+      rid: existingRid,
+      baseUrl,
+      onProgress: arg => {
+        self.setProgress(arg)
+      },
+    })
+    hits = result.hits
+    rid = result.rid
+  } else {
+    const result = await queryBlast({
+      query: cleanedSeq,
+      blastDatabase,
+      blastProgram,
+      baseUrl,
+      onProgress: arg => {
+        self.setProgress(arg)
+      },
+      onRid: r => {
+        self.setRid(r)
+      },
+    })
+    hits = result.hits
+    rid = result.rid
+  }
 
   self.setProgress('Fetching species taxonomy info...')
   const taxids = hits
@@ -79,7 +97,12 @@ export async function doLaunchBlast({
     treeMetadata: treeMetadataJson,
     rid,
     geneId: selectedTranscript?.get('parentId'),
-    transcriptId: selectedTranscript?.get('id'),
+    transcriptId: selectedTranscript?.id(),
+    transcriptName:
+      selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
+    geneName:
+      selectedTranscript?.get('gene_name') ??
+      selectedTranscript?.get('parentId'),
   })
 
   return {

package/src/MsaViewPanel/model.ts

@@ -94,6 +94,7 @@ export interface BlastParams {
   blastProgram: string
   selectedTranscript?: Feature
   proteinSequence: string
+  rid?: string
 }
 
 /**

package/src/index.ts

@@ -36,8 +36,7 @@ export default class MsaViewPlugin extends Plugin {
     }
   }
 
-  // @ts-expect-error
-  rootConfigurationSchema(pluginManager: PluginManager) {
+  rootConfigurationSchema = (pluginManager: PluginManager) => {
     return {
       msa: ConfigurationSchema('MSA', {
         datasets: types.maybe(

package/src/utils/blastCache.ts

@@ -17,6 +17,8 @@ export interface CachedBlastResult {
   timestamp: number
   geneId?: string
   transcriptId?: string
+  transcriptName?: string
+  geneName?: string
 }
 
 async function getDB() {
@@ -36,21 +38,33 @@ function createCacheKey(
   proteinSequence: string,
   blastDatabase: string,
   blastProgram: string,
+  transcriptId?: string,
 ) {
-  return `${blastDatabase}:${blastProgram}:${proteinSequence.slice(0, 100)}`
+  const seqKey = proteinSequence.slice(0, 100)
+  if (transcriptId) {
+    return `${blastDatabase}:${blastProgram}:${transcriptId}:${seqKey}`
+  }
+  return `${blastDatabase}:${blastProgram}:${seqKey}`
 }
 
 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)
+  const id = createCacheKey(
+    proteinSequence,
+    blastDatabase,
+    blastProgram,
+    transcriptId,
+  )
   return db.get(STORE_NAME, id)
 }
 
@@ -65,6 +79,8 @@ export async function saveBlastResult({
   rid,
   geneId,
   transcriptId,
+  transcriptName,
+  geneName,
 }: {
   proteinSequence: string
   blastDatabase: string
@@ -76,9 +92,16 @@ export async function saveBlastResult({
   rid: string
   geneId?: string
   transcriptId?: string
+  transcriptName?: string
+  geneName?: string
 }) {
   const db = await getDB()
-  const id = createCacheKey(proteinSequence, blastDatabase, blastProgram)
+  const id = createCacheKey(
+    proteinSequence,
+    blastDatabase,
+    blastProgram,
+    transcriptId,
+  )
   const entry: CachedBlastResult = {
     id,
     proteinSequence,
@@ -92,6 +115,8 @@ export async function saveBlastResult({
     timestamp: Date.now(),
     geneId,
     transcriptId,
+    transcriptName,
+    geneName,
   }
   await db.put(STORE_NAME, entry)
   return entry
@@ -103,6 +128,14 @@ 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/ncbiBlast.ts

@@ -1,6 +1,30 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
 import { BlastResults } from './types'
 
+export async function queryBlastFromRid({
+  rid,
+  baseUrl,
+  onProgress,
+}: {
+  rid: string
+  baseUrl: string
+  onProgress: (arg: string) => void
+}) {
+  onProgress(`Checking BLAST status for RID: ${rid}...`)
+  await waitForRid({
+    rid,
+    onProgress,
+    baseUrl,
+  })
+  const ret = await jsonfetch<BlastResults>(
+    `${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
+  )
+  return {
+    rid,
+    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
+  }
+}
+
 export async function queryBlast({
   query,
   blastDatabase,

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.2.7'
+export const version = '2.2.11'