@jbrowse/core 4.1.13 → 4.1.14

package/esm/BaseFeatureWidget/util.d.ts

@@ -6,6 +6,7 @@ export interface Feat {
     type?: string;
     name?: string;
     id?: string;
+    phase?: number;
 }
 export interface ParentFeat extends Feat {
     uniqueId: string;
@@ -33,6 +34,7 @@ export declare function revlist(list: Feat[], seqlen: number): {
     type?: string;
     name?: string;
     id?: string;
+    phase?: number;
 }[];
 export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
     type: string;
@@ -40,6 +42,7 @@ export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
     end: number;
     name?: string;
     id?: string;
+    phase?: number;
 }[];
 export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
     type: string;

package/esm/TextSearch/TextSearchManager.d.ts

@@ -12,6 +12,7 @@ export default class TextSearchManager {
     pluginManager: PluginManager;
     adapterCache: QuickLRU<string, BaseTextSearchAdapter>;
     constructor(pluginManager: PluginManager);
+    clearCache(): void;
     loadTextSearchAdapters(searchScope: SearchScope): Promise<BaseTextSearchAdapter[]>;
     relevantAdapters(searchScope: SearchScope): ({
         [x: string]: any;

package/esm/TextSearch/TextSearchManager.js

@@ -9,6 +9,9 @@ export default class TextSearchManager {
     constructor(pluginManager) {
         this.pluginManager = pluginManager;
     }
+    clearCache() {
+        this.adapterCache.clear();
+    }
     loadTextSearchAdapters(searchScope) {
         return Promise.all(this.relevantAdapters(searchScope).map(async (conf) => {
             const adapterId = readConfObject(conf, 'textSearchAdapterId');

package/esm/util/convertCodingSequenceToPeptides.js

@@ -1,8 +1,9 @@
 import { stitch } from "../BaseFeatureWidget/util.js";
 export function convertCodingSequenceToPeptides({ cds, sequence, codonTable, }) {
+    const phase = cds[0]?.phase ?? 0;
     const str = stitch(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
+    let protein = phase > 0 ? '&' : '';
+    for (let i = phase; i < str.length; i += 3) {
         protein += codonTable[str.slice(i, i + 3)] || '&';
     }
     return protein;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "4.1.13",
+  "version": "4.1.14",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -476,11 +476,11 @@
     "@emotion/react": "^11.14.0",
     "@emotion/serialize": "^1.3.3",
     "@emotion/utils": "^1.4.2",
-    "@floating-ui/react": "^0.27.18",
+    "@floating-ui/react": "^0.27.19",
     "@gmod/abortable-promise-cache": "^3.0.4",
     "@gmod/bgzf-filehandle": "^6.0.12",
     "@gmod/http-range-fetcher": "^5.0.7",
-    "@jbrowse/jexl": "^3.0.1",
+    "@jbrowse/jexl": "^3.0.2",
     "@jbrowse/mobx-state-tree": "^5.5.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "@leeoniya/ufuzzy": "^1.0.19",
@@ -488,14 +488,14 @@
     "@mui/material": "^7.3.8",
     "@mui/system": "^7.3.8",
     "@mui/types": "^7.4.11",
-    "@mui/x-data-grid": "^8.27.1",
+    "@mui/x-data-grid": "^8.27.3",
     "@types/file-saver-es": "^2.0.3",
     "canvas-sequencer-ts": "^3.1.3",
     "canvas2svg": "^1.0.16",
     "copy-to-clipboard": "^3.3.3",
     "deepmerge": "^4.3.1",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.3.1",
+    "dompurify": "^3.3.2",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-saver-es": "^2.0.5",