jbrowse-plugin-msaview 2.10.2 → 3.0.0

package/dist/utils/ncbiDomains.d.ts

@@ -5,39 +5,11 @@ export type DomainMatch = InterProScanResults['matches'][number];
  * domain and site annotations, keyed by both the versioned and primary
  * accession so callers can look up by whichever NCBI returned.
  */
-export declare function parseCddDomains(xml: string): Map<string, {
-    signature: {
-        entry?: {
-            name: string;
-            description: string;
-            accession: string;
-            featureType?: string;
-        };
-    };
-    locations: {
-        start: number;
-        end: number;
-        strand?: number;
-    }[];
-}[]>;
+export declare function parseCddDomains(xml: string): Map<string, import("msa-parsers").InterProScanMatch[]>;
 /**
  * Fetch pre-computed CDD domain and site annotations for NCBI protein
  * accessions. These come baked into the GenPept records, so a single batched
  * efetch returns them with no job submission or polling. Results are cached in
  * IndexedDB so reopening a view doesn't refetch.
  */
-export declare function fetchProteinDomains(accessions: string[]): Promise<Map<string, {
-    signature: {
-        entry?: {
-            name: string;
-            description: string;
-            accession: string;
-            featureType?: string;
-        };
-    };
-    locations: {
-        start: number;
-        end: number;
-        strand?: number;
-    }[];
-}[]>>;
+export declare function fetchProteinDomains(accessions: string[]): Promise<Map<string, import("msa-parsers").InterProScanMatch[]>>;

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.10.2";
+export declare const version = "3.0.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.10.2';
+export const version = '3.0.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.10.2",
+  "version": "3.0.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -43,7 +43,7 @@
     "git-cliff": "^2.13.1",
     "mobx": "^6.16.1",
     "mobx-react": "^9.2.2",
-    "msa-parsers": "^5.10.0",
+    "msa-parsers": "^6.0.0",
     "pixelmatch": "^7.2.0",
     "pngjs": "^7.0.0",
     "prettier": "^3.9.6",
@@ -51,7 +51,7 @@
     "puppeteer": "^25.3.0",
     "react": "^19.2.8",
     "react-dom": "^19.2.8",
-    "react-msaview": "^5.10.0",
+    "react-msaview": "^6.0.0",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -128,15 +128,15 @@ export function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel) {
  * Once an accession-bearing alignment is present (fresh from BLAST or restored
  * from cache), fetch NCBI CDD domains for those accessions and overlay them.
  * Runs once per view; the domainsRequested guard prevents refiring when NCBI
- * returns no domains (which leaves interProAnnotations undefined).
+ * returns no domains (which leaves the annotation list empty).
  */
 export function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel) {
-  const { rows, domainsRequested, interProAnnotations } = self
+  const { rows, domainsRequested, annotations } = self
   const hasAccessions = self.data.treeMetadata?.includes('"Accession"') ?? false
   if (
     rows.length > 0 &&
     hasAccessions &&
-    !interProAnnotations &&
+    annotations.length === 0 &&
     !domainsRequested
   ) {
     self.setDomainsRequested(true)

package/src/MsaViewPanel/model.ts

@@ -180,7 +180,7 @@ export default function stateModelFactory() {
         /**
          * #volatile
          * guards the one-shot auto-fetch of protein domains so it doesn't refire
-         * when NCBI returns no domains (leaving interProAnnotations undefined)
+         * when NCBI returns no domains (leaving the annotation list empty)
          */
         domainsRequested: false,
       }),

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.10.2'
+export const version = '3.0.0'