jbrowse-plugin-msaview 2.2.7 → 2.2.11

package/dist/utils/blastCache.d.ts

@@ -11,13 +11,16 @@ export interface CachedBlastResult {
     timestamp: number;
     geneId?: string;
     transcriptId?: string;
+    transcriptName?: string;
+    geneName?: string;
 }
-export declare function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, }: {
+export declare function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, transcriptId, }: {
     proteinSequence: string;
     blastDatabase: string;
     blastProgram: string;
+    transcriptId?: string;
 }): Promise<any>;
-export declare function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, }: {
+export declare function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, transcriptName, geneName, }: {
     proteinSequence: string;
     blastDatabase: string;
     blastProgram: string;
@@ -28,7 +31,10 @@ export declare function saveBlastResult({ proteinSequence, blastDatabase, blastP
     rid: string;
     geneId?: string;
     transcriptId?: string;
+    transcriptName?: string;
+    geneName?: string;
 }): Promise<CachedBlastResult>;
 export declare function getAllCachedResults(): Promise<any[]>;
+export declare function getCachedResultsByGeneId(geneId: string): Promise<any[]>;
 export declare function deleteCachedResult(id: string): Promise<void>;
 export declare function clearAllCachedResults(): Promise<void>;

package/dist/utils/blastCache.js

@@ -14,17 +14,21 @@ async function getDB() {
         },
     });
 }
-function createCacheKey(proteinSequence, blastDatabase, blastProgram) {
-    return `${blastDatabase}:${blastProgram}:${proteinSequence.slice(0, 100)}`;
+function createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId) {
+    const seqKey = proteinSequence.slice(0, 100);
+    if (transcriptId) {
+        return `${blastDatabase}:${blastProgram}:${transcriptId}:${seqKey}`;
+    }
+    return `${blastDatabase}:${blastProgram}:${seqKey}`;
 }
-export async function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, }) {
+export async function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, transcriptId, }) {
     const db = await getDB();
-    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram);
+    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId);
     return db.get(STORE_NAME, id);
 }
-export async function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, }) {
+export async function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, transcriptName, geneName, }) {
     const db = await getDB();
-    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram);
+    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId);
     const entry = {
         id,
         proteinSequence,
@@ -38,6 +42,8 @@ export async function saveBlastResult({ proteinSequence, blastDatabase, blastPro
         timestamp: Date.now(),
         geneId,
         transcriptId,
+        transcriptName,
+        geneName,
     };
     await db.put(STORE_NAME, entry);
     return entry;
@@ -47,6 +53,13 @@ export async function getAllCachedResults() {
     const results = await db.getAll(STORE_NAME);
     return results.toSorted((a, b) => b.timestamp - a.timestamp);
 }
+export async function getCachedResultsByGeneId(geneId) {
+    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) {
     const db = await getDB();
     await db.delete(STORE_NAME, id);

package/dist/utils/blastCache.js.map

@@ -1 +1 @@
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+{"version":3,"file":"blastCache.js","sourceRoot":"","sources":["../../src/utils/blastCache.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,KAAK,CAAA;AAE5B,MAAM,OAAO,GAAG,6BAA6B,CAAA;AAC7C,MAAM,UAAU,GAAG,eAAe,CAAA;AAClC,MAAM,UAAU,GAAG,CAAC,CAAA;AAmBpB,KAAK,UAAU,KAAK;IAClB,OAAO,MAAM,CAAC,OAAO,EAAE,UAAU,EAAE;QACjC,OAAO,CAAC,EAAE,EAAE,UAAU;YACpB,IAAI,UAAU,GAAG,CAAC,IAAI,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC/D,EAAE,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC;YACD,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC9C,EAAE,CAAC,iBAAiB,CAAC,UAAU,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;YACrD,CAAC;QACH,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,cAAc,CACrB,eAAuB,EACvB,aAAqB,EACrB,YAAoB,EACpB,YAAqB;IAErB,MAAM,MAAM,GAAG,eAAe,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IAC5C,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,YAAY,IAAI,MAAM,EAAE,CAAA;IACrE,CAAC;IACD,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,MAAM,EAAE,CAAA;AACrD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,GAMb;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,OAAO,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,EACpC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,EACZ,GAAG,EACH,IAAI,EACJ,YAAY,EACZ,GAAG,EACH,MAAM,EACN,YAAY,EACZ,cAAc,EACd,QAAQ,GAcT;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,MAAM,KAAK,GAAsB;QAC/B,EAAE;QACF,eAAe;QACf,aAAa;QACb,YAAY;QACZ,YAAY;QACZ,GAAG;QACH,IAAI;QACJ,YAAY;QACZ,GAAG;QACH,SAAS,EAAE,IAAI,CAAC,GAAG,EAAE;QACrB,MAAM;QACN,YAAY;QACZ,cAAc;QACd,QAAQ;KACT,CAAA;IACD,MAAM,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,mBAAmB;IACvC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAC9D,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAAC,MAAc;IAC3D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO;SACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC;SAChC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAClD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EAAU;IACjD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AACjC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,qBAAqB;IACzC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,CAAA;AAC5B,CAAC"}

package/dist/utils/ncbiBlast.d.ts

@@ -1,3 +1,16 @@
+export declare function queryBlastFromRid({ rid, baseUrl, onProgress, }: {
+    rid: string;
+    baseUrl: string;
+    onProgress: (arg: string) => void;
+}): Promise<{
+    rid: string;
+    hits: {
+        description: import("./types").BlastHitDescription[];
+        hsps: {
+            hseq: string;
+        }[];
+    }[];
+}>;
 export declare function queryBlast({ query, blastDatabase, blastProgram, baseUrl, onProgress, onRid, }: {
     query: string;
     blastDatabase: string;

package/dist/utils/ncbiBlast.js

@@ -1,4 +1,17 @@
 import { jsonfetch, textfetch, timeout } from './fetch';
+export async function queryBlastFromRid({ rid, baseUrl, onProgress, }) {
+    onProgress(`Checking BLAST status for RID: ${rid}...`);
+    await waitForRid({
+        rid,
+        onProgress,
+        baseUrl,
+    });
+    const ret = await jsonfetch(`${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, blastProgram, baseUrl, onProgress, onRid, }) {
     onProgress('Submitting to NCBI BLAST...');
     const { rid } = await initialQuery({

package/dist/utils/ncbiBlast.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ncbiBlast.js","sourceRoot":"","sources":["../../src/utils/ncbiBlast.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAGvD,MAAM,CAAC,KAAK,UAAU,iBAAiB,CAAC,EACtC,GAAG,EACH,OAAO,EACP,UAAU,GAKX;IACC,UAAU,CAAC,kCAAkC,GAAG,KAAK,CAAC,CAAA;IACtD,MAAM,UAAU,CAAC;QACf,GAAG;QACH,UAAU;QACV,OAAO;KACR,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,OAAO,gBAAgB,GAAG,8CAA8C,CAC5E,CAAA;IACD,OAAO;QACL,GAAG;QACH,IAAI,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,EAAE;KAC5D,CAAA;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,EAC/B,KAAK,EACL,aAAa,EACb,YAAY,EACZ,OAAO,EACP,UAAU,EACV,KAAK,GAQN;IACC,UAAU,CAAC,6BAA6B,CAAC,CAAA;IACzC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,YAAY,CAAC;QACjC,KAAK;QACL,aAAa;QACb,YAAY;QACZ,OAAO;KACR,CAAC,CAAA;IACF,KAAK,CAAC,GAAG,CAAC,CAAA;IACV,MAAM,UAAU,CAAC;QACf,GAAG;QACH,UAAU;QACV,OAAO;KACR,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,OAAO,gBAAgB,GAAG,8CAA8C,CAC5E,CAAA;IACD,OAAO;QACL,GAAG;QACH,IAAI,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,EAAE;KAC5D,CAAA;AACH,CAAC;AAED,KAAK,UAAU,YAAY,CAAC,EAC1B,KAAK,EACL,YAAY,EACZ,aAAa,EACb,OAAO,GAMR;IACC,MAAM,GAAG,GAAG,MAAM,SAAS,CAAC,OAAO,EAAE;QACnC,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,GAAG,EAAE,KAAK;YACV,OAAO,EAAE,YAAY,KAAK,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,YAAY;YAClE,QAAQ,EAAE,aAAa;YACvB,KAAK,EAAE,KAAK;YACZ,GAAG,CAAC,aAAa,KAAK,kBAAkB;gBACtC,CAAC,CAAC;oBACE,YAAY,EAAE,IAAI;oBAClB,OAAO,EAAE,wBAAwB;iBAClC;gBACH,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,YAAY,KAAK,cAAc;gBACjC,CAAC,CAAC,EAAE,cAAc,EAAE,YAAY,EAAE;gBAClC,CAAC,CAAC,EAAE,CAAC;SACR,CAAC;KACH,CAAC,CAAA;IAEF,4EAA4E;IAC5E,qEAAqE;IACrE,8DAA8D;IAC9D,MAAM,GAAG,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAEhD,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;IACzD,CAAC;IACD,OAAO;QACL,GAAG;QACH,IAAI;KACL,CAAA;AACH,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EACxB,GAAG,EACH,UAAU,EACV,OAAO,GAKR;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;YAC9B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,kCAAkC,IAAI,GAAG,CAAC,EAAE,CAAC,CAAA;QAC1D,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,OAAO,yCAAyC,GAAG,EAAE,CACzD,CAAA;QACD,MAAM,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,OAAO,GAAG,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,OAAO,GAAG,sBAAsB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAEhD,IAAI,SAAS,EAAE,CAAC;YACd,SAAQ;QACV,CAAC;QAED,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,IAAI,KAAK,CAAC,SAAS,GAAG,SAAS,CAAC,CAAA;QACxC,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,IAAI,OAAO,EAAE,CAAC;gBACZ,OAAO,IAAI,CAAA;YACb,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.2.7";
+export declare const version = "2.2.11";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.2.7';
+export const version = '2.2.11';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.2.7",
+  "version": "2.2.11",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -35,7 +35,7 @@
     "g2p_mapper": "^2.0.0",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.0",
-    "react-msaview": "^5.0.6",
+    "react-msaview": "^5.0.7",
     "swr": "^2.3.8"
   },
   "devDependencies": {
@@ -56,8 +56,8 @@
     "eslint-plugin-import": "^2.32.0",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.0.1",
-    "eslint-plugin-react-refresh": "^0.4.26",
-    "eslint-plugin-unicorn": "^62.0.0",
+    "eslint-plugin-react-refresh": "^0.5.2",
+    "eslint-plugin-unicorn": "^63.0.0",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "prettier": "^3.7.4",
@@ -69,8 +69,8 @@
     "rxjs": "^7.8.2",
     "serve": "^14.2.5",
     "tss-react": "^4.9.20",
-    "typescript": "^5.9.3",
-    "typescript-eslint": "^8.54.0",
-    "vitest": "^4.0.16"
+    "typescript": "^6.0.2",
+    "typescript-eslint": "^8.57.2",
+    "vitest": "^4.1.1"
   }
 }

package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx

@@ -76,6 +76,7 @@ const EnsemblGeneTree = observer(function ({
         <TranscriptSelector
           feature={feature}
           options={options}
+          selectedId={selectedId}
           selectedTranscript={selectedTranscript}
           onTranscriptChange={setSelectedId}
           proteinSequence={proteinSequence}

package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx

@@ -59,6 +59,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
   const [querySeqName, setQuerySeqName] = useState('')
   const {
     options,
+    selectedId,
     setSelectedId,
     selectedTranscript,
     proteinSequence,
@@ -143,6 +144,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
         <TranscriptSelector
           feature={feature}
           options={options}
+          selectedId={selectedId}
           selectedTranscript={selectedTranscript}
           onTranscriptChange={setSelectedId}
           proteinSequence={proteinSequence}

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

@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react'
+import React, { useEffect, useMemo, useState } from 'react'
 
 import { Feature, getContainingView } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
@@ -24,6 +24,31 @@ import type { CachedBlastResult } from '../../../utils/blastCache'
 import type { AbstractTrackModel } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
+function getGeneIdentifiers(feature: Feature): string[] {
+  const ids = [
+    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)]
+}
+
+function getResultDisplayName(result: CachedBlastResult): string {
+  const parts = []
+  if (result.geneName) {
+    parts.push(result.geneName)
+  }
+  if (result.transcriptName && result.transcriptName !== result.geneName) {
+    parts.push(result.transcriptName)
+  }
+  if (parts.length === 0) {
+    parts.push(result.geneId ?? result.transcriptId ?? 'Unknown')
+  }
+  return parts.join(' - ')
+}
+
 const CachedBlastResults = observer(function ({
   model,
   handleClose,
@@ -37,19 +62,20 @@ const CachedBlastResults = observer(function ({
   const [loading, setLoading] = useState(true)
   const view = getContainingView(model) as LinearGenomeViewModel
 
-  const geneId = feature.get('id')
+  const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
+
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
         const cached = await getAllCachedResults()
-        setResults(cached.filter(r => r.geneId === geneId))
+        setResults(cached.filter(r => r.geneId && geneIds.includes(r.geneId)))
         setLoading(false)
       } catch (e) {
         console.error(e)
       }
     })()
-  }, [geneId])
+  }, [geneIds])
 
   const handleDelete = async (id: string) => {
     await deleteCachedResult(id)
@@ -65,7 +91,7 @@ const CachedBlastResults = observer(function ({
     blastLaunchViewFromCache({
       view,
       cached,
-      newViewTitle: `BLAST - ${cached.geneId ?? cached.transcriptId ?? 'Unknown gene'}`,
+      newViewTitle: `BLAST - ${getResultDisplayName(cached)}`,
     })
     handleClose()
   }
@@ -132,7 +158,7 @@ const CachedBlastResults = observer(function ({
               }}
             >
               <ListItemText
-                primary={`${result.geneId ?? result.transcriptId ?? 'Unknown'} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`}
+                primary={`${getResultDisplayName(result)} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`}
                 secondary={`${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...`}
               />
             </ListItemButton>

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

@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react'
+import React, { useEffect, useMemo, useState } from 'react'
 
 import { ErrorMessage } from '@jbrowse/core/ui'
 import {
@@ -30,6 +30,17 @@ import { useTranscriptSelection } from '../useTranscriptSelection'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
+function getGeneIdentifiers(feature: Feature): string[] {
+  const ids = [
+    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)]
+}
+
 const useStyles = makeStyles()({
   dialogContent: {
     width: '80em',
@@ -72,22 +83,25 @@ const NCBIBlastAutomaticPanel = observer(function ({
   const [hasCachedResults, setHasCachedResults] = useState(false)
   const [error, setError] = useState<unknown>()
 
-  const geneId = feature.get('id')
+  const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
         const results = await getAllCachedResults()
-        setHasCachedResults(results.some(r => r.geneId === geneId))
+        setHasCachedResults(
+          results.some(r => r.geneId && geneIds.includes(r.geneId)),
+        )
       } catch (e) {
         console.error(e)
         setError(e)
       }
     })()
-  }, [geneId])
+  }, [geneIds])
 
   const {
     options,
+    selectedId,
     setSelectedId,
     selectedTranscript,
     proteinSequence,
@@ -180,6 +194,7 @@ const NCBIBlastAutomaticPanel = observer(function ({
         <TranscriptSelector
           feature={feature}
           options={options}
+          selectedId={selectedId}
           selectedTranscript={selectedTranscript}
           onTranscriptChange={setSelectedId}
           proteinSequence={proteinSequence}

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

@@ -43,8 +43,14 @@ const NCBIBlastManualPanel = observer(function ({
 }) {
   const { classes } = useStyles()
   const view = getContainingView(model) as LinearGenomeViewModel
-  const { options, setSelectedId, selectedTranscript, proteinSequence, error } =
-    useTranscriptSelection({ feature, view })
+  const {
+    options,
+    selectedId,
+    setSelectedId,
+    selectedTranscript,
+    proteinSequence,
+    error,
+  } = useTranscriptSelection({ feature, view })
 
   const s2 = cleanProteinSequence(proteinSequence)
   const link = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${s2}`
@@ -59,6 +65,7 @@ const NCBIBlastManualPanel = observer(function ({
         <TranscriptSelector
           feature={feature}
           options={options}
+          selectedId={selectedId}
           selectedTranscript={selectedTranscript}
           onTranscriptChange={setSelectedId}
           proteinSequence={proteinSequence}

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

@@ -21,13 +21,14 @@ export default function NCBIBlastMethodSelector({
         <FormControlLabel
           value="automatic"
           control={<Radio />}
-          label="Run NCBI BLAST and load results automatically"
+          label="Automatic"
         />
         <FormControlLabel
-          value="manual"
+          value="rid"
           control={<Radio />}
-          label="Link to NCBI BLAST and import results manually"
+          label="Load from RID"
         />
+        <FormControlLabel value="manual" control={<Radio />} label="Manual" />
       </RadioGroup>
     </FormControl>
   )

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

@@ -7,11 +7,18 @@ import { IconButton } from '@mui/material'
 import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel'
 import NCBIBlastManualPanel from './NCBIBlastManualPanel'
 import NCBIBlastMethodSelector from './NCBIBlastMethodSelector'
+import NCBIBlastRIDPanel from './NCBIBlastRIDPanel'
 import NCBISettingsDialog from './NCBISettingsDialog'
 import { BASE_BLAST_URL } from './consts'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
+const panelMap = {
+  automatic: NCBIBlastAutomaticPanel,
+  rid: NCBIBlastRIDPanel,
+  manual: NCBIBlastManualPanel,
+} as const
+
 export default function NCBIBlastPanel({
   handleClose,
   model,
@@ -28,10 +35,7 @@ export default function NCBIBlastPanel({
   )
   const [settingsOpen, setSettingsOpen] = useState(false)
 
-  const Panel =
-    lookupMethod === 'automatic'
-      ? NCBIBlastAutomaticPanel
-      : NCBIBlastManualPanel
+  const Panel = panelMap[lookupMethod as keyof typeof panelMap]
 
   return (
     <>

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

@@ -0,0 +1,187 @@
+import React, { useState } from 'react'
+
+import { ErrorMessage } from '@jbrowse/core/ui'
+import {
+  AbstractTrackModel,
+  Feature,
+  getContainingView,
+} from '@jbrowse/core/util'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  MenuItem,
+  Typography,
+} from '@mui/material'
+import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
+
+import { blastLaunchView } from './blastLaunchView'
+import ExternalLink from '../../../components/ExternalLink'
+import TextField2 from '../../../components/TextField2'
+import { getGeneDisplayName, getTranscriptDisplayName } from '../../util'
+import TranscriptSelector from '../TranscriptSelector'
+import { useTranscriptSelection } from '../useTranscriptSelection'
+
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+const useStyles = makeStyles()({
+  dialogContent: {
+    width: '80em',
+  },
+})
+
+const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'] as const
+
+type msaAlgorithmsT = (typeof msaAlgorithms)[number]
+
+const NCBIBlastRIDPanel = observer(function ({
+  handleClose,
+  feature,
+  model,
+  children,
+  baseUrl,
+}: {
+  model: AbstractTrackModel
+  feature: Feature
+  baseUrl: string
+  handleClose: () => void
+  children: React.ReactNode
+}) {
+  const { classes } = useStyles()
+  const view = getContainingView(model) as LinearGenomeViewModel
+  const [launchViewError, setLaunchViewError] = useState<unknown>()
+  const [rid, setRid] = useState('')
+  const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] =
+    useState<msaAlgorithmsT>('clustalo')
+
+  const {
+    options,
+    selectedId,
+    setSelectedId,
+    selectedTranscript,
+    proteinSequence,
+    error: proteinSequenceError,
+  } = useTranscriptSelection({ feature, view })
+
+  const e = proteinSequenceError ?? launchViewError
+  const style = { width: 150 }
+  const trimmedRid = rid.trim()
+
+  return (
+    <>
+      <DialogContent className={classes.dialogContent}>
+        {children}
+        {e ? <ErrorMessage error={e} /> : null}
+
+        <Typography variant="body2" style={{ marginBottom: 16 }}>
+          Enter the RID (Request ID) from a previously submitted NCBI BLAST
+          query. You can find the RID in the BLAST results page URL or at the
+          top of the results page. RIDs are typically valid for 24-36 hours
+          after submission.
+        </Typography>
+
+        <TextField2
+          variant="outlined"
+          label="BLAST RID"
+          placeholder="e.g., ABC12345"
+          fullWidth
+          style={{ marginBottom: 16 }}
+          value={rid}
+          onChange={event => {
+            setRid(event.target.value)
+          }}
+        />
+
+        {trimmedRid ? (
+          <Typography variant="body2" style={{ marginBottom: 16 }}>
+            <ExternalLink href={`${baseUrl}?CMD=Get&RID=${trimmedRid}`}>
+              View BLAST results on NCBI
+            </ExternalLink>
+          </Typography>
+        ) : null}
+
+        <TextField2
+          variant="outlined"
+          label="MSA Algorithm"
+          style={style}
+          select
+          value={selectedMsaAlgorithm}
+          onChange={event => {
+            setSelectedMsaAlgorithm(
+              event.target.value as (typeof msaAlgorithms)[number],
+            )
+          }}
+        >
+          {msaAlgorithms.map(val => (
+            <MenuItem value={val} key={val}>
+              {val}
+            </MenuItem>
+          ))}
+        </TextField2>
+
+        <TranscriptSelector
+          feature={feature}
+          options={options}
+          selectedId={selectedId}
+          selectedTranscript={selectedTranscript}
+          onTranscriptChange={setSelectedId}
+          proteinSequence={proteinSequence}
+        />
+
+        <Typography style={{ marginTop: 20 }}>
+          This will fetch the BLAST results for the provided RID and run them
+          through a multiple sequence alignment. The protein sequence from the
+          selected transcript will be added as the query sequence in the MSA.
+        </Typography>
+      </DialogContent>
+      <DialogActions>
+        <Button
+          color="primary"
+          variant="contained"
+          onClick={() => {
+            try {
+              if (!selectedTranscript || !trimmedRid) {
+                return
+              }
+              setLaunchViewError(undefined)
+              blastLaunchView({
+                feature: selectedTranscript,
+                view,
+                newViewTitle: `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                blastParams: {
+                  baseUrl,
+                  blastProgram: 'blastp',
+                  blastDatabase: 'nr',
+                  msaAlgorithm: selectedMsaAlgorithm,
+                  selectedTranscript,
+                  proteinSequence,
+                  rid: trimmedRid,
+                },
+              })
+            } catch (e) {
+              console.error(e)
+              setLaunchViewError(e)
+            }
+
+            handleClose()
+          }}
+          disabled={!proteinSequence || !trimmedRid}
+        >
+          Submit
+        </Button>
+        <Button
+          color="secondary"
+          variant="contained"
+          onClick={() => {
+            handleClose()
+          }}
+        >
+          Cancel
+        </Button>
+      </DialogActions>
+    </>
+  )
+})
+
+export default NCBIBlastRIDPanel

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

@@ -146,6 +146,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
                 <TranscriptSelector
                   feature={feature}
                   options={transcripts}
+                  selectedId={selectedId}
                   selectedTranscript={selectedTranscript}
                   onTranscriptChange={setSelectedId}
                   proteinSequence={proteinSequence}