jbrowse-plugin-msaview 2.7.0 → 2.7.2

package/dist/utils/useLocalStorage.d.ts

@@ -0,0 +1 @@
+export declare function useLocalStorage<T>(key: string, initialValue: T): readonly [T, (value: T) => void];

package/dist/utils/useLocalStorage.js

@@ -0,0 +1,29 @@
+import { useState } from 'react';
+// Vendored rather than imported from `@jbrowse/core/util`: that barrel is
+// host-provided, and a barrel split dropped this export, making the BLAST panel
+// throw "(0, PR.useLocalStorage) is not a function" on hosts built during that
+// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes
+// this plugin out of the whack-a-mole.
+function readLocalStorage(key, initialValue) {
+    try {
+        const item = globalThis.localStorage.getItem(key);
+        return item === null ? initialValue : JSON.parse(item);
+    }
+    catch (error) {
+        console.error(error);
+        return initialValue;
+    }
+}
+export function useLocalStorage(key, initialValue) {
+    const [storedValue, setStoredValue] = useState(() => readLocalStorage(key, initialValue));
+    const setValue = (value) => {
+        setStoredValue(value);
+        try {
+            globalThis.localStorage.setItem(key, JSON.stringify(value));
+        }
+        catch (error) {
+            console.error(error);
+        }
+    };
+    return [storedValue, setValue];
+}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.7.0";
+export declare const version = "2.7.2";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.7.0';
+export const version = '2.7.2';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.7.0",
+  "version": "2.7.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -20,7 +20,6 @@
     "@gmod/bgzf-filehandle": "^6.2.0",
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
-    "react-msaview": "^5.6.1",
     "swr": "^2.4.2"
   },
   "devDependencies": {
@@ -52,6 +51,7 @@
     "puppeteer": "^25.3.0",
     "react": "^19.2.8",
     "react-dom": "^19.2.8",
+    "react-msaview": "^5.6.3",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",
@@ -74,7 +74,9 @@
     "test:setup:version": "node scripts/test-versions.mjs setup",
     "test:versions": "node scripts/test-versions.mjs run",
     "test:version": "node scripts/test-versions.mjs run",
-    "preversion": "pnpm lint",
+    "host-compat": "node scripts/host-compat-probe.mjs --bundle dist/jbrowse-plugin-msaview.umd.production.min.js",
+    "check-ci": "node scripts/require-green-ci.mjs",
+    "preversion": "pnpm check-ci && pnpm lint && pnpm build && pnpm host-compat",
     "version": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add src/version.ts",
     "postversion": "git push --follow-tags"
   }

package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx

@@ -1,6 +1,5 @@
 import React, { useState } from 'react'
 
-import { useLocalStorage } from '@jbrowse/core/util'
 import SettingsIcon from '@mui/icons-material/Settings'
 import { IconButton } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
@@ -11,6 +10,7 @@ import NCBIBlastMethodSelector from './NCBIBlastMethodSelector'
 import NCBIBlastRIDPanel from './NCBIBlastRIDPanel'
 import NCBISettingsDialog from './NCBISettingsDialog'
 import { BASE_BLAST_URL } from './consts'
+import { useLocalStorage } from '../../../utils/useLocalStorage'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 

package/src/LaunchMsaView/components/calculateProteinSequence.ts

@@ -1,35 +1,39 @@
-import {
-  dedupe,
-  defaultCodonTable,
-  generateCodonTable,
-  revcom,
-} from '@jbrowse/core/util'
+import { dedupe, revcom } from '@jbrowse/core/util'
+import { convertCodingSequenceToPeptides } from '@jbrowse/core/util/convertCodingSequenceToPeptides'
+
+import { getGeneticCode, parseTranslTable } from './geneticCodes'
 
 import type { Feat } from './types'
 import type { Feature } from '@jbrowse/core/util'
 
-// pure constant: the standard codon table never varies, so build it once rather
-// than on every translation (which runs on every panel re-render)
-const codonTable = generateCodonTable(defaultCodonTable)
-
-export function stitch(subfeats: Feat[], sequence: string) {
-  return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('')
-}
+// `@jbrowse/core/util/convertCodingSequenceToPeptides` is a deep path, so unlike
+// the `@jbrowse/core/util` barrel it is absent from ReExports and gets bundled
+// rather than resolved out of the host's JBrowseExports. That is what makes
+// reusing core's translation safe across every host a config names: this module
+// previously built its codon table at module scope from the barrel's
+// `defaultCodonTable`, and a core build that dropped that export turned it into
+// `Object.keys(undefined)` while the UMD was still evaluating -- the plugin
+// global was never assigned and PluginLoader error-paged the whole app.
 
 export function calculateProteinSequence({
   cds,
   sequence,
+  geneticCodeId,
 }: {
   cds: Feat[]
   sequence: string
+  geneticCodeId?: number
 }) {
-  const str = stitch(cds, sequence)
-  let protein = ''
-  for (let i = 0; i < str.length; i += 3) {
-    // use & symbol for undefined codon, or partial slice
-    protein += codonTable[str.slice(i, i + 3)] ?? '&'
-  }
-  return protein
+  // `starts` is deliberately not passed: @jbrowse/core 4.3.0's signature has no
+  // such parameter, so alternative initiators (GTG under table 11, ATA under
+  // table 2) render as their internal residue rather than M. Core main added it;
+  // pass it here when msaview's @jbrowse/core floor reaches that release.
+  const { codonTable } = getGeneticCode(geneticCodeId)
+  return convertCodingSequenceToPeptides({
+    cds,
+    sequence,
+    codonTable,
+  })
 }
 
 export function revlist(list: Feat[], seqlen: number) {
@@ -62,8 +66,19 @@ export function getProteinSequenceFromFeature({
     feat => `${feat.start}-${feat.end}`,
   )
 
+  // a mitochondrial gene declares e.g. transl_table=2, so it translates with
+  // NCBI table 2 rather than the standard code. GFF3 usually carries the
+  // attribute on the CDS rather than the transcript, so check both.
+  const cdsSubfeature = feature
+    .get('subfeatures')
+    ?.find((f: Feature) => f.get('type')?.toLowerCase() === 'cds')
+  const geneticCodeId =
+    parseTranslTable(feature.get('transl_table')) ??
+    parseTranslTable(cdsSubfeature?.get('transl_table'))
+
   return calculateProteinSequence({
     cds: strand === -1 ? revlist(cds, seq.length) : cds,
     sequence: strand === -1 ? revcom(seq) : seq,
+    geneticCodeId,
   })
 }

package/src/LaunchMsaView/components/geneticCodes.ts

@@ -0,0 +1,298 @@
+// NCBI translation tables (genetic codes), copied verbatim from
+// jbrowse-components packages/core/src/util/geneticCodes.ts, which parses them
+// from NCBI's authoritative gc.prt. `ncbieaa` gives the amino acid for each of
+// the 64 codons in a fixed base order; `sncbieaa` marks valid start codons.
+//
+// Vendored rather than imported: core exports this only on main, and the msaview
+// bundle has to translate the same way on every host a config names, back to
+// v4.0.0. Replace the whole file with a re-export of
+// `@jbrowse/core/util/geneticCodes` once a release ships it -- that path is not
+// in ReExports, so it bundles rather than binding to the host.
+export interface NcbiGeneticCode {
+  id: number
+  name: string
+  ncbieaa: string
+  sncbieaa: string
+}
+
+export const ncbiGeneticCodes: NcbiGeneticCode[] = [
+  {
+    id: 1,
+    name: 'Standard',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 2,
+    name: 'Vertebrate Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--------------------MMMM----------**---M------------',
+  },
+  {
+    id: 3,
+    name: 'Yeast Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**----------------------MM---------------M------------',
+  },
+  {
+    id: 4,
+    name: 'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--MM------**-------M------------MMMM---------------M------------',
+  },
+  {
+    id: 5,
+    name: 'Invertebrate Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--------------------MMMM---------------M------------',
+  },
+  {
+    id: 6,
+    name: 'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 9,
+    name: 'Echinoderm Mitochondrial; Flatworm Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M---------------M------------',
+  },
+  {
+    id: 10,
+    name: 'Euplotid Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M----------------------------',
+  },
+  {
+    id: 11,
+    name: 'Bacterial, Archaeal and Plant Plastid',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--*----M------------MMMM---------------M------------',
+  },
+  {
+    id: 12,
+    name: 'Alternative Yeast Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 13,
+    name: 'Ascidian Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**----------------------MM---------------M------------',
+  },
+  {
+    id: 14,
+    name: 'Alternative Flatworm Mitochondrial',
+    ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '-----------*-----------------------M----------------------------',
+  },
+  {
+    id: 15,
+    name: 'Blepharisma Macronuclear',
+    ncbieaa: 'FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------*---*--------------------M----------------------------',
+  },
+  {
+    id: 16,
+    name: 'Chlorophycean Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------*---*--------------------M----------------------------',
+  },
+  {
+    id: 21,
+    name: 'Trematode Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M---------------M------------',
+  },
+  {
+    id: 22,
+    name: 'Scenedesmus obliquus Mitochondrial',
+    ncbieaa: 'FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '------*---*---*--------------------M----------------------------',
+  },
+  {
+    id: 23,
+    name: 'Thraustochytrium Mitochondrial',
+    ncbieaa: 'FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--*-------**--*-----------------M--M---------------M------------',
+  },
+  {
+    id: 24,
+    name: 'Rhabdopleuridae Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**-------M---------------M---------------M------------',
+  },
+  {
+    id: 25,
+    name: 'Candidate Division SR1 and Gracilibacteria',
+    ncbieaa: 'FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**-----------------------M---------------M------------',
+  },
+  {
+    id: 26,
+    name: 'Pachysolen tannophilus Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 27,
+    name: 'Karyorelict Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 28,
+    name: 'Condylostoma Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*--------------------M----------------------------',
+  },
+  {
+    id: 29,
+    name: 'Mesodinium Nuclear',
+    ncbieaa: 'FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 30,
+    name: 'Peritrich Nuclear',
+    ncbieaa: 'FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 31,
+    name: 'Blastocrithidia Nuclear',
+    ncbieaa: 'FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M----------------------------',
+  },
+  {
+    id: 32,
+    name: 'Balanophoraceae Plastid',
+    ncbieaa: 'FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------*---*----M------------MMMM---------------M------------',
+  },
+  {
+    id: 33,
+    name: 'Cephalodiscidae Mitochondrial',
+    ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M-------*-------M---------------M---------------M------------',
+  },
+]
+
+// The codon order shared by every NCBI table -- the Base1/Base2/Base3 comment
+// rows in gc.prt. codon i = BASE1[i] + BASE2[i] + BASE3[i].
+const BASE1 = 'TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG'
+const BASE2 = 'TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG'
+const BASE3 = 'TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG'
+
+const CODONS = Array.from(
+  { length: 64 },
+  (_, i) => BASE1[i]! + BASE2[i]! + BASE3[i]!,
+)
+
+const ncbiCodeById = new Map(ncbiGeneticCodes.map(t => [t.id, t]))
+
+export interface GeneticCode {
+  id: number
+  name: string
+  // case-insensitive codon -> amino acid letter, '*' for a stop codon
+  codonTable: Record<string, string>
+  // valid start codons (uppercase)
+  starts: string[]
+}
+
+// Expand an uppercase codon map so every case combination of a triplet resolves,
+// which is what callers reading raw sequence need.
+function caseExpand(table: Record<string, string>) {
+  const out: Record<string, string> = {}
+  for (const [codon, aa] of Object.entries(table)) {
+    const cases = (i: number) => {
+      const n = codon.charAt(i)
+      return [n.toUpperCase(), n.toLowerCase()]
+    }
+    for (const n0 of cases(0)) {
+      for (const n1 of cases(1)) {
+        for (const n2 of cases(2)) {
+          out[n0 + n1 + n2] = aa
+        }
+      }
+    }
+  }
+  return out
+}
+
+function buildGeneticCode(id: number): GeneticCode {
+  const def = ncbiCodeById.get(id)
+  if (!def && id !== 1) {
+    console.warn(
+      `Unknown genetic code (transl_table=${id}); using standard code`,
+    )
+  }
+  const {
+    id: resolvedId,
+    name,
+    ncbieaa,
+    sncbieaa,
+  } = def ?? ncbiCodeById.get(1)!
+  const table: Record<string, string> = {}
+  const starts: string[] = []
+  for (const [i, codon] of CODONS.entries()) {
+    table[codon] = ncbieaa[i]!
+    if (sncbieaa[i] === 'M') {
+      starts.push(codon)
+    }
+  }
+  return { id: resolvedId, name, codonTable: caseExpand(table), starts }
+}
+
+const geneticCodeCache = new Map<number, GeneticCode>()
+
+// Resolves the codon map + start set for an NCBI translation-table id, falling
+// back to the standard code (1) for an unrecognized id. Memoized: there are only
+// ~27 tables and each result is immutable.
+export function getGeneticCode(id = 1): GeneticCode {
+  let code = geneticCodeCache.get(id)
+  if (!code) {
+    code = buildGeneticCode(id)
+    geneticCodeCache.set(id, code)
+  }
+  return code
+}
+
+// Parses a GFF/GenBank `transl_table` attribute value into an NCBI table id. The
+// GFF adapter yields a string (or an array if the attribute repeated), so this
+// normalizes both; returns undefined for a missing or non-positive-integer value
+// so callers fall back to their default code.
+export function parseTranslTable(value: unknown): number | undefined {
+  const raw = Array.isArray(value) ? value[0] : value
+  const n = Number(raw)
+  return Number.isInteger(n) && n > 0 ? n : undefined
+}

package/src/LaunchMsaView/components/types.ts

@@ -2,6 +2,9 @@ export interface Feat {
   start: number
   end: number
   type?: string
+  // GFF phase of the first coding base; convertCodingSequenceToPeptides reads it
+  // off cds[0] to start translation in the right frame
+  phase?: number
 }
 
 export interface SeqState {

package/src/LaunchMsaView/index.ts

@@ -15,8 +15,9 @@ function isDisplay(elt: { name: string }): elt is DisplayType {
 }
 
 // The canvas LinearBasicDisplay (JBrowse >=4.3) exposes the right-clicked
-// feature via contextMenuInfo + async fetchFullFeature rather than a synchronous
-// feature object.
+// feature via contextMenuInfo + async fetchFullFeature. Hosts before that -- and
+// the v3.7.0 in the wild that shipped configs still name -- expose it
+// synchronously as contextMenuFeature, and only have that one.
 interface ContextMenuInfo {
   item: { featureId: string; type?: string }
   displayedRegionIndex: number
@@ -25,13 +26,16 @@ interface ContextMenuInfo {
 interface DisplayModel {
   contextMenuItems: () => MenuItem[]
   contextMenuInfo?: ContextMenuInfo
-  isGeneLike: boolean
-  fetchFullFeature: (
+  isGeneLike?: boolean
+  fetchFullFeature?: (
     featureId: string,
     displayedRegionIndex: number,
   ) => Promise<Feature | undefined>
+  contextMenuFeature?: Feature
 }
 
+const GENE_LIKE_TYPES = new Set(['gene', 'mRNA', 'transcript'])
+
 function extendStateModel(stateModel: IAnyModelType) {
   return stateModel.views((self: DisplayModel) => {
     const superContextMenuItems = self.contextMenuItems
@@ -39,40 +43,45 @@ function extendStateModel(stateModel: IAnyModelType) {
       contextMenuItems() {
         const track = getContainingTrack(self)
         const session = getSession(track)
+        const launch = (feature: Feature) => {
+          session.queueDialog(handleClose => [
+            LaunchMsaViewDialog,
+            { model: track, handleClose, feature },
+          ])
+        }
+
         const info = self.contextMenuInfo
-        const showMsaMenuItem = info && self.isGeneLike
+        const fetchFullFeature = self.fetchFullFeature
+        const legacyFeature = self.contextMenuFeature
+        const onClick =
+          info && fetchFullFeature && self.isGeneLike
+            ? () => {
+                fetchFullFeature(info.item.featureId, info.displayedRegionIndex)
+                  .then(feature => {
+                    if (feature) {
+                      launch(feature)
+                    } else {
+                      session.notify(
+                        'Could not load feature for MSA view',
+                        'warning',
+                      )
+                    }
+                  })
+                  .catch((e: unknown) => {
+                    session.notifyError(`${e}`, e)
+                  })
+              }
+            : legacyFeature &&
+                GENE_LIKE_TYPES.has(String(legacyFeature.get('type')))
+              ? () => {
+                  launch(legacyFeature)
+                }
+              : undefined
+
         return [
           ...superContextMenuItems(),
-          ...(showMsaMenuItem
-            ? [
-                {
-                  label: 'Launch MSA view',
-                  icon: AddIcon,
-                  onClick: () => {
-                    self
-                      .fetchFullFeature(
-                        info.item.featureId,
-                        info.displayedRegionIndex,
-                      )
-                      .then(feature => {
-                        if (feature) {
-                          session.queueDialog(handleClose => [
-                            LaunchMsaViewDialog,
-                            { model: track, handleClose, feature },
-                          ])
-                        } else {
-                          session.notify(
-                            'Could not load feature for MSA view',
-                            'warning',
-                          )
-                        }
-                      })
-                      .catch((e: unknown) => {
-                        session.notifyError(`${e}`, e)
-                      })
-                  },
-                },
-              ]
+          ...(onClick
+            ? [{ label: 'Launch MSA view', icon: AddIcon, onClick }]
             : []),
         ]
       },

package/src/MsaViewPanel/model.ts

@@ -77,7 +77,12 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        querySeqName: types.stripDefault(types.string, 'QUERY'),
+        // Plain defaults, not types.stripDefault: that postdates the
+        // mobx-state-tree every released core exposes (present only on main), and
+        // the missing function throws while this model is being built, which
+        // error-pages the whole app rather than just this view. Restore
+        // stripDefault once a release ships it.
+        querySeqName: 'QUERY',
 
         /**
          * #property
@@ -87,7 +92,8 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        zoomToBaseLevel: types.stripDefault(types.boolean, false),
+        // see querySeqName above re: types.stripDefault
+        zoomToBaseLevel: false,
 
         /**
          * #property

package/src/utils/useLocalStorage.ts

@@ -0,0 +1,31 @@
+import { useState } from 'react'
+
+// Vendored rather than imported from `@jbrowse/core/util`: that barrel is
+// host-provided, and a barrel split dropped this export, making the BLAST panel
+// throw "(0, PR.useLocalStorage) is not a function" on hosts built during that
+// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes
+// this plugin out of the whack-a-mole.
+function readLocalStorage<T>(key: string, initialValue: T): T {
+  try {
+    const item = globalThis.localStorage.getItem(key)
+    return item === null ? initialValue : (JSON.parse(item) as T)
+  } catch (error) {
+    console.error(error)
+    return initialValue
+  }
+}
+
+export function useLocalStorage<T>(key: string, initialValue: T) {
+  const [storedValue, setStoredValue] = useState<T>(() =>
+    readLocalStorage(key, initialValue),
+  )
+  const setValue = (value: T) => {
+    setStoredValue(value)
+    try {
+      globalThis.localStorage.setItem(key, JSON.stringify(value))
+    } catch (error) {
+      console.error(error)
+    }
+  }
+  return [storedValue, setValue] as const
+}

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.7.0'
+export const version = '2.7.2'