@jbrowse/core 4.2.1 → 4.3.0

package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -1,7 +1,5 @@
-import { stringifyBED } from './saveTrackFileTypes/bed.ts';
-import { stringifyGBK } from './saveTrackFileTypes/genbank.ts';
-import { stringifyGFF3 } from './saveTrackFileTypes/gff3.ts';
 import type PluginManager from '../../PluginManager.ts';
+import type { FileTypeExporter } from './saveTrackFileTypes/types.ts';
 import type { AnyConfigurationSchemaType } from '../../configuration/index.ts';
 import type { MenuItem } from '../../ui/index.ts';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
@@ -42,24 +40,7 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
     hideDisplay(displayId: string): number;
     replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: {}): void;
 } & {
-    saveTrackFileFormatOptions(): {
-        gff3: {
-            name: string;
-            extension: string;
-            callback: typeof stringifyGFF3;
-        };
-        genbank: {
-            name: string;
-            extension: string;
-            callback: typeof stringifyGBK;
-            helpText: string;
-        };
-        bed: {
-            name: string;
-            extension: string;
-            callback: typeof stringifyBED;
-        };
-    };
+    saveTrackFileFormatOptions(): Record<string, FileTypeExporter>;
 } & {
     trackMenuItems(): MenuItem[];
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{

package/esm/ui/SanitizedHTML.js

@@ -18,6 +18,7 @@ const htmlTags = [
     'i',
     'img',
     'li',
+    'mark',
     'p',
     'pre',
     'span',

package/esm/util/tracks.d.ts

@@ -66,10 +66,10 @@ export interface AdapterConfig {
     [key: string]: unknown;
 }
 export type AdapterGuesser = (file: FileLocation, index?: FileLocation, adapterHint?: string) => AdapterConfig | undefined;
-export type TrackTypeGuesser = (adapterName: string) => string | undefined;
+export type TrackTypeGuesser = (adapterName: string, file?: FileLocation) => string | undefined;
 export declare function getFileName(track: FileLocation): string;
 export declare function guessAdapter(file: FileLocation, index: FileLocation | undefined, adapterHint?: string, model?: IAnyStateTreeNode): AdapterConfig;
-export declare function guessTrackType(adapterType: string, model?: IAnyStateTreeNode): string;
+export declare function guessTrackType(adapterType: string, model?: IAnyStateTreeNode, file?: FileLocation): string;
 export declare function generateUnsupportedTrackConf(trackName: string, trackUrl: string, categories: string[] | undefined): {
     type: string;
     name: string;

package/esm/util/tracks.js

@@ -232,13 +232,13 @@ export function guessAdapter(file, index, adapterHint, model) {
         type: UNKNOWN,
     };
 }
-export function guessTrackType(adapterType, model) {
+export function guessTrackType(adapterType, model, file) {
     if (model) {
         const session = getSession(model);
         const trackTypeGuesser = getEnv(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
             return undefined;
         });
-        const trackType = trackTypeGuesser(adapterType);
+        const trackType = trackTypeGuesser(adapterType, file);
         if (trackType) {
             return trackType;
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "4.2.1",
+  "version": "4.3.0",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -478,15 +478,15 @@
     "@emotion/utils": "^1.4.2",
     "@floating-ui/react": "^0.27.19",
     "@gmod/abortable-promise-cache": "^3.0.4",
-    "@gmod/bgzf-filehandle": "^6.0.18",
+    "@gmod/bgzf-filehandle": "^6.0.19",
     "@gmod/http-range-fetcher": "^5.0.7",
     "@jbrowse/jexl": "^3.0.2",
     "@jbrowse/mobx-state-tree": "^5.6.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "@leeoniya/ufuzzy": "^1.0.19",
-    "@mui/icons-material": "^7.3.10",
-    "@mui/material": "^7.3.10",
-    "@mui/system": "^7.3.10",
+    "@mui/icons-material": "^7.3.11",
+    "@mui/material": "^7.3.11",
+    "@mui/system": "^7.3.11",
     "@mui/types": "^7.4.12",
     "@mui/x-data-grid": "^8.28.2",
     "@types/file-saver-es": "^2.0.3",
@@ -495,14 +495,14 @@
     "copy-to-clipboard": "^3.3.3",
     "deepmerge": "^4.3.1",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.4.0",
+    "dompurify": "^3.4.2",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-saver-es": "^2.0.5",
-    "generic-filehandle2": "^2.1.4",
+    "generic-filehandle2": "^2.1.7",
     "idb": "^8.0.3",
     "librpc-web-mod": "^2.1.1",
-    "mobx": "^6.15.0",
+    "mobx": "^6.15.3",
     "mobx-react": "^9.2.1",
     "react-draggable": "^4.5.0",
     "rxjs": "^7.8.2",