jbrowse-plugin-msaview 2.3.8 → 2.4.0

package/dist/utils/blastCache.d.ts

@@ -1,9 +1,10 @@
+import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
 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;
@@ -14,17 +15,11 @@ export interface CachedBlastResult {
     transcriptName?: string;
     geneName?: string;
 }
-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, transcriptName, geneName, }: {
     proteinSequence: string;
-    blastDatabase: string;
-    blastProgram: string;
-    msaAlgorithm: string;
+    blastDatabase: BlastDatabase;
+    blastProgram: BlastProgram;
+    msaAlgorithm: MsaAlgorithm;
     msa: string;
     tree: string;
     treeMetadata: string;
@@ -35,6 +30,5 @@ export declare function saveBlastResult({ proteinSequence, blastDatabase, blastP
     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

@@ -20,11 +20,6 @@ function createCacheKey(proteinSequence, blastDatabase, blastProgram, transcript
     }
     return `${blastDatabase}:${blastProgram}:${proteinSequence}`;
 }
-export async function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, transcriptId, }) {
-    const db = await getDB();
-    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, transcriptName, geneName, }) {
     const db = await getDB();
     const id = createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId);
@@ -52,13 +47,6 @@ 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;AAQ5B,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,aAA4B,EAC5B,YAA0B,EAC1B,YAAqB;IAErB,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,YAAY,IAAI,eAAe,EAAE,CAAA;IAC9E,CAAC;IACD,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,eAAe,EAAE,CAAA;AAC9D,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,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/msa.d.ts

@@ -1,5 +1,6 @@
+import type { MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
 export declare function launchMSA({ algorithm, sequence, onProgress, }: {
-    algorithm: string;
+    algorithm: MsaAlgorithm;
     sequence: string;
     onProgress: (arg: string) => void;
 }): Promise<{

package/dist/utils/msa.js

@@ -40,9 +40,6 @@ async function wait({ onProgress, jobId, algorithm, }) {
 }
 export async function launchMSA({ algorithm, sequence, onProgress, }) {
     const config = algorithms[algorithm];
-    if (!config) {
-        throw new Error(`unknown algorithm: ${algorithm}`);
-    }
     onProgress(`Launching ${algorithm} MSA...`);
     const jobId = await textfetch(`${base}/${algorithm}/run`, {
         method: 'POST',

package/dist/utils/msa.js.map

@@ -1 +1 @@
-{"version":3,"file":"msa.js","sourceRoot":"","sources":["../../src/utils/msa.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAE5C,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,MAAM,UAAU,GAOZ;IACF,QAAQ,EAAE;QACR,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE;QAC1C,SAAS,EAAE,iBAAiB;QAC5B,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE;QACxE,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;CACF,CAAA;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,SAAS,GAKV;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,gCAAgC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,EAAE,CAAC,CAAA;QAEtE,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAC1B,MAAK;QACP,CAAC;aAAM,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAC9B,SAAS,EACT,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,MAAM,GAAG,UAAU,CAAC,SAAS,CAAC,CAAA;IACpC,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,sBAAsB,SAAS,EAAE,CAAC,CAAA;IACpD,CAAC;IAED,UAAU,CAAC,aAAa,SAAS,SAAS,CAAC,CAAA;IAE3C,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,MAAM,EAAE;QACxD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC;KAC1D,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,CAAC,CAAA;IAC5C,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAClB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAC3D;QACD,IAAI,EAAE,MAAM,SAAS,CACnB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,UAAU,EAAE,CAC5D;KACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"msa.js","sourceRoot":"","sources":["../../src/utils/msa.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAI5C,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,MAAM,UAAU,GAOZ;IACF,QAAQ,EAAE;QACR,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE;QAC1C,SAAS,EAAE,iBAAiB;QAC5B,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE;QACxE,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,MAAM,EAAE;QACN,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,EAAE,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,SAAS,EAAE;QAC5D,SAAS,EAAE,IAAI;QACf,UAAU,EAAE,WAAW;KACxB;CACF,CAAA;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,SAAS,GAKV;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,gCAAgC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,EAAE,CAAC,CAAA;QAEtE,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAC1B,MAAK;QACP,CAAC;aAAM,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAC9B,SAAS,EACT,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,MAAM,GAAG,UAAU,CAAC,SAAS,CAAC,CAAA;IAEpC,UAAU,CAAC,aAAa,SAAS,SAAS,CAAC,CAAA;IAE3C,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,MAAM,EAAE;QACxD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC;KAC1D,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,CAAC,CAAA;IAC5C,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAClB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAC3D;QACD,IAAI,EAAE,MAAM,SAAS,CACnB,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,IAAI,MAAM,CAAC,UAAU,EAAE,CAC5D;KACF,CAAA;AACH,CAAC"}

package/dist/utils/ncbiBlast.d.ts

@@ -1,3 +1,4 @@
+import type { BlastDatabase, BlastProgram } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
 export declare function queryBlastFromRid({ rid, baseUrl, onProgress, }: {
     rid: string;
     baseUrl: string;
@@ -13,8 +14,8 @@ export declare function queryBlastFromRid({ rid, baseUrl, onProgress, }: {
 }>;
 export declare function queryBlast({ query, blastDatabase, blastProgram, baseUrl, onProgress, onRid, }: {
     query: string;
-    blastDatabase: string;
-    blastProgram: string;
+    blastDatabase: BlastDatabase;
+    blastProgram: BlastProgram;
     baseUrl: string;
     onProgress: (arg: string) => void;
     onRid: (arg: string) => void;

package/dist/utils/ncbiBlast.js

@@ -31,7 +31,7 @@ async function initialQuery({ query, blastProgram, blastDatabase, baseUrl, }) {
             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',

package/dist/utils/ncbiBlast.js.map

@@ -1 +1 @@
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package/dist/utils/taxonomyNames.js

@@ -12,9 +12,12 @@ async function getDB() {
         },
     });
 }
-async function getCachedCommonName(taxid) {
+async function getCachedTaxonomies(taxids) {
     const db = await getDB();
-    return db.get(STORE_NAME, taxid);
+    const tx = db.transaction(STORE_NAME, 'readonly');
+    const results = await Promise.all(taxids.map(taxid => tx.store.get(taxid)));
+    await tx.done;
+    return results;
 }
 async function saveTaxonomyCache(entries) {
     const db = await getDB();
@@ -27,8 +30,10 @@ async function saveTaxonomyCache(entries) {
 export async function fetchTaxonomyInfo(taxids) {
     const result = new Map();
     const uncachedTaxids = [];
-    for (const taxid of taxids) {
-        const cached = await getCachedCommonName(taxid);
+    const cachedResults = await getCachedTaxonomies(taxids);
+    for (let i = 0; i < taxids.length; i++) {
+        const taxid = taxids[i];
+        const cached = cachedResults[i];
         if (cached) {
             result.set(taxid, {
                 sciname: cached.sciname,

package/dist/utils/taxonomyNames.js.map

@@ -1 +1 @@
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+{"version":3,"file":"taxonomyNames.js","sourceRoot":"","sources":["../../src/utils/taxonomyNames.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,KAAK,CAAA;AAE5B,MAAM,OAAO,GAAG,gCAAgC,CAAA;AAChD,MAAM,UAAU,GAAG,cAAc,CAAA;AACjC,MAAM,UAAU,GAAG,CAAC,CAAA;AAQpB,KAAK,UAAU,KAAK;IAClB,OAAO,MAAM,CAAC,OAAO,EAAE,UAAU,EAAE;QACjC,OAAO,CAAC,EAAE;YACR,IAAI,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC7C,EAAE,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC;YACD,EAAE,CAAC,iBAAiB,CAAC,UAAU,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,CAAA;QACxD,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,KAAK,UAAU,mBAAmB,CAAC,MAAgB;IACjD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;IACjD,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,GAAG,CAC/B,MAAM,CAAC,GAAG,CACR,KAAK,CAAC,EAAE,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAwC,CACpE,CACF,CAAA;IACD,MAAM,EAAE,CAAC,IAAI,CAAA;IACb,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,KAAK,UAAU,iBAAiB,CAAC,OAAyB;IACxD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,EAAE,WAAW,CAAC,CAAA;IAClD,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,MAAM,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC3B,CAAC;IACD,MAAM,EAAE,CAAC,IAAI,CAAA;AACf,CAAC;AAOD,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,MAAgB;IAEhB,MAAM,MAAM,GAAG,IAAI,GAAG,EAAwB,CAAA;IAC9C,MAAM,cAAc,GAAa,EAAE,CAAA;IACnC,MAAM,aAAa,GAAG,MAAM,mBAAmB,CAAC,MAAM,CAAC,CAAA;IAEvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE;gBAChB,OAAO,EAAE,MAAM,CAAC,OAAO;gBACvB,UAAU,EAAE,MAAM,CAAC,UAAU;aAC9B,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC;IACH,CAAC;IAED,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,SAAS,GAAG,GAAG,CAAA;IACrB,MAAM,OAAO,GAAqB,EAAE,CAAA;IAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QAC1D,MAAM,KAAK,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAEhC,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAC1B,4EAA4E,QAAQ,cAAc,CACnG,CAAA;YACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;YAElC,iEAAiE;YACjE,uEAAuE;YACvE,2CAA2C;YAC3C,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAkB,CAAA;YAC1C,MAAM,UAAU,GAAG,kCAAkC,CAAA;YACrD,IAAI,KAAK,CAAA;YACT,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;gBAChD,MAAM,YAAY,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;gBACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,CAAA;gBAE5B,+DAA+D;gBAC/D,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,MAAM,GAAG,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACvC,OAAO,KAAK,GAAG,CAAC,IAAI,MAAM,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;oBACzC,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,MAAM,CAAC,CAAA;oBACjD,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;oBACnD,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;wBACtB,MAAK;oBACP,CAAC;oBACD,IAAI,SAAS,KAAK,CAAC,CAAC,IAAI,SAAS,GAAG,UAAU,EAAE,CAAC;wBAC/C,KAAK,EAAE,CAAA;wBACP,MAAM,GAAG,SAAS,GAAG,CAAC,CAAA;oBACxB,CAAC;yBAAM,CAAC;wBACN,KAAK,EAAE,CAAA;wBACP,MAAM,GAAG,UAAU,GAAG,CAAC,CAAA;oBACzB,CAAC;gBACH,CAAC;gBAED,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAA;gBAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBAC3C,MAAM,YAAY,GAAG,QAAQ,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAA;gBACrD,MAAM,oBAAoB,GAAG,QAAQ,EAAE,QAAQ,CAAC,aAAa,CAAC,CAAA;gBAC9D,IAAI,CAAC,QAAQ,IAAI,CAAC,YAAY,IAAI,CAAC,oBAAoB,CAAC,EAAE,CAAC;oBACzD,QAAQ,CAAC,GAAG,CAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YAED,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;gBAC1B,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBACpC,IAAI,QAAQ,EAAE,CAAC;oBACb,MAAM,aAAa,GACjB,+CAA+C,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;oBAChE,MAAM,UAAU,GAAG,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;oBACnE,MAAM,OAAO,GAAG,yCAAyC,CAAC,IAAI,CAC5D,QAAQ,CACT,CAAA;oBACD,MAAM,IAAI,GAAG,aAAa,EAAE,CAAC,CAAC,CAAC,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,CAAA;oBAElD,MAAM,GAAG,GAAG,OAAO,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;oBAC9B,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,EAAE,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAA;oBACrD,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAA;gBACzD,CAAC;qBAAM,CAAC;oBACN,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,EAAE,UAAU,EAAE,SAAS,EAAE,CAAC,CAAA;gBAC7D,CAAC;YACH,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,KAAK,CAAC,gCAAgC,EAAE,KAAK,CAAC,CAAA;QACxD,CAAC;IACH,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,MAAM,iBAAiB,CAAC,OAAO,CAAC,CAAA;IAClC,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.3.8";
+export declare const version = "2.4.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.3.8';
+export const version = '2.4.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.3.8",
+  "version": "2.4.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -17,7 +17,7 @@
   ],
   "dependencies": {
     "@emotion/styled": "^11.14.1",
-    "g2p_mapper": "^2.0.1",
+    "g2p_mapper": "^2.0.2",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
     "react-msaview": "^5.0.16",
@@ -27,37 +27,37 @@
     "@emotion/react": "^11.14.0",
     "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^4.2.0",
+    "@jbrowse/core": "^4.2.1",
     "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@jbrowse/plugin-linear-genome-view": "^4.2.0",
-    "@mui/icons-material": "^7.3.10",
-    "@mui/material": "^7.3.10",
-    "@mui/system": "^7.3.10",
-    "@mui/x-data-grid": "^8.28.2",
-    "@types/node": "^25.6.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.2.1",
+    "@mui/icons-material": "^7.3.11",
+    "@mui/material": "^7.3.11",
+    "@mui/system": "^7.3.11",
+    "@mui/x-data-grid": "^8.28.5",
+    "@types/node": "^25.7.0",
     "@types/react": "^19.2.14",
-    "@typescript-eslint/eslint-plugin": "^8.59.1",
-    "@typescript-eslint/parser": "^8.59.1",
+    "@typescript-eslint/eslint-plugin": "^8.59.3",
+    "@typescript-eslint/parser": "^8.59.3",
     "esbuild": "^0.28.0",
-    "eslint": "^10.2.1",
+    "eslint": "^10.3.0",
     "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.1.1",
     "eslint-plugin-unicorn": "^64.0.0",
-    "mobx": "^6.15.0",
+    "mobx": "^6.15.3",
     "mobx-react": "^9.2.1",
     "prettier": "^3.8.3",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^24.42.0",
-    "react": "^19.2.5",
-    "react-dom": "^19.2.5",
+    "puppeteer": "^24.43.1",
+    "react": "^19.2.6",
+    "react-dom": "^19.2.6",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",
-    "tss-react": "^4.9.20",
+    "tss-react": "^4.9.21",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.59.1",
-    "vitest": "^4.1.5"
+    "typescript-eslint": "^8.59.3",
+    "vitest": "^4.1.6"
   },
   "scripts": {
     "clean": "rimraf dist",
@@ -73,6 +73,8 @@
     "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",
-    "release": "node scripts/release.mjs"
+    "preversion": "pnpm lint",
+    "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/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -3,7 +3,7 @@ import React from 'react'
 import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
-import { useStyles } from './util'
+import { hasHoverPosition, useStyles } from './util'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -12,25 +12,11 @@ const GenomeMouseoverHighlight = observer(function ({
 }: {
   model: LinearGenomeViewModel
 }) {
-  const session = getSession(model)
-  const { hovered, views } = session
-
-  // Early return if no MSA view exists
+  const { hovered, views } = getSession(model)
   const hasMsaView = views.some(s => s.type === 'MsaView')
-  if (!hasMsaView) {
-    return null
-  }
-
-  // Early return if no hover position
-  if (
-    !hovered ||
-    typeof hovered !== 'object' ||
-    !('hoverPosition' in hovered)
-  ) {
-    return null
-  }
-
-  return <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />
+  return hasMsaView && hasHoverPosition(hovered) ? (
+    <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />
+  ) : null
 })
 
 const GenomeMouseoverHighlightRenderer = observer(function ({
@@ -38,7 +24,7 @@ const GenomeMouseoverHighlightRenderer = observer(function ({
   hovered,
 }: {
   model: LinearGenomeViewModel
-  hovered: object & Record<'hoverPosition', unknown>
+  hovered: { hoverPosition: unknown }
 }) {
   const { classes } = useStyles()
   const { offsetPx } = model
@@ -48,7 +34,7 @@ const GenomeMouseoverHighlightRenderer = observer(function ({
   }
 
   const s = model.bpToPx({ refName, coord: coord - 1 })
-  const e = model.bpToPx({ refName, coord: coord })
+  const e = model.bpToPx({ refName, coord })
 
   if (s && e) {
     const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -3,32 +3,32 @@ import React from 'react'
 import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
-import { useStyles } from './util'
+import { hasHoverPosition, useStyles } from './util'
 
 import type { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
 
-// Outer component: only re-renders when MSA view or highlights change
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
   model,
 }: {
   model: LGV
 }) {
-  const { views } = getSession(model)
+  const { views, hovered } = getSession(model)
   const msaView = views.find(f => f.type === 'MsaView') as
     | JBrowsePluginMsaViewModel
     | undefined
-
   const highlights = msaView?.connectedHighlights
 
-  // Early return if no highlights - avoid all other work
-  if (!highlights || highlights.length === 0) {
-    return null
-  }
-
-  return <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />
+  // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
+  // handles the single-bp display in that case
+  return !hasHoverPosition(hovered) && highlights?.length ? (
+    <MsaToGenomeHighlightRenderer
+      model={model}
+      highlights={Array.from(highlights)}
+    />
+  ) : null
 })
 
 // Inner component: handles the scroll-dependent rendering

package/src/AddHighlightModel/util.ts

@@ -1,5 +1,11 @@
 import { makeStyles } from 'tss-react/mui'
 
+export function hasHoverPosition(
+  hovered: unknown,
+): hovered is { hoverPosition: unknown } {
+  return !!hovered && typeof hovered === 'object' && 'hoverPosition' in hovered
+}
+
 export const useStyles = makeStyles()({
   highlight: {
     height: '100%',

package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -1,17 +1,15 @@
 import React, { useState } from 'react'
 
-import { readConfObject } from '@jbrowse/core/configuration'
 import { Dialog } from '@jbrowse/core/ui'
 import { getSession } from '@jbrowse/core/util'
 import { Tab, Tabs } from '@mui/material'
 
-import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree'
 import ManualMSALoader from './ManualMSALoader/ManualMSALoader'
 import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
+import { readMsaDatasets } from './PreLoadedMSA/types'
 import TabPanel from './TabPanel'
 
-import type { Dataset } from './PreLoadedMSA/types'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 export default function LaunchMsaViewDialog({
@@ -24,11 +22,8 @@ export default function LaunchMsaViewDialog({
   model: AbstractTrackModel
 }) {
   const session = getSession(model)
-  const { jbrowse } = session
-  const datasets = readConfObject(jbrowse, ['msa', 'datasets']) as
-    | Dataset[]
-    | undefined
-  const hasPreloadedDatasets = datasets && datasets.length > 0
+  const datasets = readMsaDatasets(session.jbrowse)
+  const hasPreloadedDatasets = !!datasets?.length
 
   const [value, setValue] = useState('ncbi_blast')
 
@@ -43,7 +38,6 @@ export default function LaunchMsaViewDialog({
         {hasPreloadedDatasets ? (
           <Tab label="Pre-loaded MSA datasets" value="preloaded_msa" />
         ) : null}
-        <Tab label="Ensembl GeneTree" value="ensembl_genetree" />
         <Tab label="Manual upload" value="manual_msa" />
       </Tabs>
       <TabPanel value={value} index="ncbi_blast">
@@ -62,13 +56,6 @@ export default function LaunchMsaViewDialog({
           />
         </TabPanel>
       ) : null}
-      <TabPanel value={value} index="ensembl_genetree">
-        <EnsemblGeneTree
-          model={model}
-          feature={feature}
-          handleClose={handleClose}
-        />
-      </TabPanel>
       <TabPanel value={value} index="manual_msa">
         <ManualMSALoader
           model={model}

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

@@ -77,10 +77,10 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
     setSelectedId,
     selectedTranscript,
     proteinSequence,
-    error: error2,
+    error,
   } = useTranscriptSelection({ feature, view })
 
-  const e = launchViewError ?? error2
+  const e = launchViewError ?? error
   return (
     <>
       <DialogContent className={classes.dialogContent}>
@@ -198,17 +198,13 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
           }
           onClick={() => {
             try {
-              if (!selectedTranscript) {
-                return
-              }
-
               setLaunchViewError(undefined)
               launchView({
                 session,
                 newViewTitle: getGeneDisplayName(selectedTranscript),
                 view,
-                feature: selectedTranscript,
-                querySeqName: querySeqName.trim() || undefined,
+                feature: selectedTranscript!,
+                querySeqName: querySeqName.trim(),
                 ...(inputMethod === 'file'
                   ? {
                       msaFilehandle: msaFileLocation,
@@ -217,15 +213,15 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
                   : {
                       data: {
                         msa: msaText,
-                        tree: treeText || undefined,
+                        tree: treeText,
                       },
                     }),
               })
 
               handleClose()
-            } catch (e) {
-              console.error(e)
-              setLaunchViewError(e)
+            } catch (err) {
+              console.error(err)
+              setLaunchViewError(err)
             }
           }}
         >

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

@@ -18,7 +18,7 @@ import { makeStyles } from 'tss-react/mui'
 
 import CachedBlastResults from './CachedBlastResults'
 import { blastLaunchView } from './blastLaunchView'
-import { msaAlgorithms } from './consts'
+import { blastDatabaseOptions, blastPrograms, msaAlgorithms } from './consts'
 import { useCachedBlastResults } from './useCachedBlastResults'
 import TextField2 from '../../../components/TextField2'
 import {
@@ -29,7 +29,7 @@ import {
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
 
-import type { MsaAlgorithm } from './consts'
+import type { BlastDatabase, BlastProgram, MsaAlgorithm } from './consts'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -55,12 +55,6 @@ const useStyles = makeStyles()({
   },
 })
 
-const blastDatabaseOptions = ['nr', 'nr_cluster_seq'] as const
-const blastPrograms = ['blastp', 'quick-blastp'] as const
-
-type blastDatabaseOptionsT = (typeof blastDatabaseOptions)[number]
-type blastProgramsT = (typeof blastPrograms)[number]
-
 const NCBIBlastAutomaticPanel = observer(function ({
   handleClose,
   feature,
@@ -78,11 +72,11 @@ const NCBIBlastAutomaticPanel = observer(function ({
   const view = getContainingView(model) as LinearGenomeViewModel
   const [launchViewError, setLaunchViewError] = useState<unknown>()
   const [selectedBlastDatabase, setSelectedBlastDatabase] =
-    useState<blastDatabaseOptionsT>('nr')
+    useState<BlastDatabase>('nr')
   const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] =
     useState<MsaAlgorithm>('clustalo')
   const [selectedBlastProgram, setSelectedBlastProgram] =
-    useState<blastProgramsT>('quick-blastp')
+    useState<BlastProgram>('quick-blastp')
 
   const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
   const { results: cachedResults, error: cachedResultsError } =
@@ -109,8 +103,7 @@ const NCBIBlastAutomaticPanel = observer(function ({
           select
           value={selectedBlastDatabase}
           onChange={event => {
-            const newDb = event.target
-              .value as (typeof blastDatabaseOptions)[number]
+            const newDb = event.target.value as BlastDatabase
             setSelectedBlastDatabase(newDb)
             if (newDb === 'nr_cluster_seq') {
               setSelectedBlastProgram('blastp')
@@ -150,9 +143,7 @@ const NCBIBlastAutomaticPanel = observer(function ({
             select
             value={selectedBlastProgram}
             onChange={event => {
-              setSelectedBlastProgram(
-                event.target.value as (typeof blastPrograms)[number],
-              )
+              setSelectedBlastProgram(event.target.value as BlastProgram)
             }}
           >
             {blastPrograms.map(val => (

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

@@ -96,15 +96,6 @@ const NCBIBlastManualPanel = observer(function ({
           onClick={() => {
             handleClose()
           }}
-        >
-          Submit
-        </Button>
-        <Button
-          color="secondary"
-          variant="contained"
-          onClick={() => {
-            handleClose()
-          }}
         >
           Close
         </Button>

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

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util'
 
-import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model'
+import type { BlastParams } from '../../../MsaViewPanel/model'
 import type { CachedBlastResult } from '../../../utils/blastCache'
 import type { Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -14,9 +14,9 @@ export function blastLaunchView({
   newViewTitle: string
   view: LinearGenomeViewModel
   feature: Feature
-  blastParams: Record<string, unknown>
+  blastParams: BlastParams
 }) {
-  return getSession(view).addView('MsaView', {
+  getSession(view).addView('MsaView', {
     type: 'MsaView',
     displayName: newViewTitle,
     connectedViewId: view.id,
@@ -25,7 +25,7 @@ export function blastLaunchView({
     colWidth: 10,
     rowHeight: 12,
     blastParams,
-  }) as JBrowsePluginMsaViewModel
+  })
 }
 
 export function blastLaunchViewFromCache({
@@ -37,7 +37,7 @@ export function blastLaunchViewFromCache({
   view: LinearGenomeViewModel
   cached: CachedBlastResult
 }) {
-  return getSession(view).addView('MsaView', {
+  getSession(view).addView('MsaView', {
     type: 'MsaView',
     displayName: newViewTitle,
     connectedViewId: view.id,
@@ -49,5 +49,5 @@ export function blastLaunchViewFromCache({
       tree: cached.tree,
       treeMetadata: cached.treeMetadata,
     },
-  }) as JBrowsePluginMsaViewModel
+  })
 }