@jbrowse/core 2.16.1 → 2.17.0

package/BaseFeatureWidget/BaseFeatureDetail/index.d.ts

@@ -1,7 +1,5 @@
 import React from 'react';
 import { BaseCardProps, BaseProps } from '../types';
-import BaseCard from './BaseCard';
-import FeatureDetails from './FeatureDetails';
 export declare const BaseCoreDetails: (props: BaseProps) => React.JSX.Element;
 export declare const BaseAttributes: (props: BaseProps) => React.JSX.Element;
 export interface BaseInputProps extends BaseCardProps {
@@ -12,4 +10,5 @@ export interface BaseInputProps extends BaseCardProps {
 }
 declare const BaseFeatureDetail: ({ model }: BaseInputProps) => React.JSX.Element | null;
 export default BaseFeatureDetail;
-export { BaseCard, FeatureDetails };
+export { default as BaseCard } from './BaseCard';
+export { default as FeatureDetails } from './FeatureDetails';

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -13,10 +13,8 @@ const util_2 = require("../util");
 // locals
 const Attributes_1 = __importDefault(require("./Attributes"));
 const BaseCard_1 = __importDefault(require("./BaseCard"));
-exports.BaseCard = BaseCard_1.default;
 const CoreDetails_1 = __importDefault(require("./CoreDetails"));
 const FeatureDetails_1 = __importDefault(require("./FeatureDetails"));
-exports.FeatureDetails = FeatureDetails_1.default;
 const BaseCoreDetails = (props) => {
     const { title = 'Primary data' } = props;
     return (react_1.default.createElement(BaseCard_1.default, { ...props, title: title },
@@ -47,3 +45,7 @@ const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {
     }
 });
 exports.default = BaseFeatureDetail;
+var BaseCard_2 = require("./BaseCard");
+Object.defineProperty(exports, "BaseCard", { enumerable: true, get: function () { return __importDefault(BaseCard_2).default; } });
+var FeatureDetails_2 = require("./FeatureDetails");
+Object.defineProperty(exports, "FeatureDetails", { enumerable: true, get: function () { return __importDefault(FeatureDetails_2).default; } });

package/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts

@@ -1,12 +1,33 @@
 import { Instance } from 'mobx-state-tree';
 import { SimpleFeatureSerialized } from '../../util';
 export declare function SequenceFeatureDetailsF(): import("mobx-state-tree").IModelType<{}, {
+    /**
+     * #volatile
+     */
     showCoordinatesSetting: string;
+    /**
+     * #volatile
+     */
     intronBp: number;
+    /**
+     * #volatile
+     */
     upDownBp: number;
+    /**
+     * #volatile
+     */
     upperCaseCDS: boolean;
+    /**
+     * #volatile
+     */
     charactersPerRow: number;
+    /**
+     * #volatile
+     */
     feature: SimpleFeatureSerialized | undefined;
+    /**
+     * #volatile
+     */
     mode: string;
 } & {
     /**

package/BaseFeatureWidget/SequenceFeatureDetails/model.js

@@ -9,17 +9,47 @@ function localStorageGetNumber(key, defaultVal) {
     var _a;
     return +((_a = (0, util_1.localStorageGetItem)(key)) !== null && _a !== void 0 ? _a : defaultVal);
 }
+function localStorageGetBoolean(key, defaultVal) {
+    return Boolean(JSON.parse((0, util_1.localStorageGetItem)(key) || JSON.stringify(defaultVal)));
+}
+function localStorageSetNumber(key, value) {
+    (0, util_1.localStorageSetItem)(key, JSON.stringify(value));
+}
+function localStorageSetBoolean(key, value) {
+    (0, util_1.localStorageSetItem)(key, JSON.stringify(value));
+}
+const p = 'sequenceFeatureDetails';
 function SequenceFeatureDetailsF() {
     return mobx_state_tree_1.types
         .model('SequenceFeatureDetails')
         .volatile(() => ({
-        showCoordinatesSetting: (0, util_1.localStorageGetItem)('sequenceFeatureDetails-showCoordinatesSetting') ||
-            'none',
-        intronBp: localStorageGetNumber('sequenceFeatureDetails-intronBp', 10),
-        upDownBp: localStorageGetNumber('sequenceFeatureDetails-upDownBp', 100),
-        upperCaseCDS: Boolean(JSON.parse((0, util_1.localStorageGetItem)('sequenceFeatureDetails-upperCaseCDS') || 'true')),
+        /**
+         * #volatile
+         */
+        showCoordinatesSetting: (0, util_1.localStorageGetItem)(`${p}-showCoordinatesSetting`) || 'none',
+        /**
+         * #volatile
+         */
+        intronBp: localStorageGetNumber(`${p}-intronBp`, 10),
+        /**
+         * #volatile
+         */
+        upDownBp: localStorageGetNumber(`${p}-upDownBp`, 100),
+        /**
+         * #volatile
+         */
+        upperCaseCDS: localStorageGetBoolean(`${p}-upperCaseCDS`, true),
+        /**
+         * #volatile
+         */
         charactersPerRow: 100,
+        /**
+         * #volatile
+         */
         feature: undefined,
+        /**
+         * #volatile
+         */
         mode: '',
     }))
         .actions(self => ({
@@ -100,10 +130,10 @@ function SequenceFeatureDetailsF() {
         .actions(self => ({
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-upDownBp', JSON.stringify(self.upDownBp));
-                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-intronBp', JSON.stringify(self.intronBp));
-                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-upperCaseCDS', JSON.stringify(self.upperCaseCDS));
-                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-showCoordinatesSetting', self.showCoordinatesSetting);
+                localStorageSetNumber(`${p}-upDownBp`, self.upDownBp);
+                localStorageSetNumber(`${p}-intronBp`, self.intronBp);
+                localStorageSetBoolean(`${p}-upperCaseCDS`, self.upperCaseCDS);
+                (0, util_1.localStorageSetItem)(`${p}-showCoordinatesSetting`, self.showCoordinatesSetting);
             }));
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 self.setMode(self.hasCDS ? 'cds' : self.hasExon ? 'cdna' : 'genomic');

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -179,8 +179,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 }>;
 export type BaseFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts

@@ -125,4 +125,9 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * is)
      */
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<FeatureDensityStats>;
+    getSources(regions: Region[]): Promise<{
+        name: string;
+        color?: string;
+        [key: string]: unknown;
+    }[]>;
 }

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js

@@ -170,5 +170,15 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
         }
         return this.getRegionFeatureDensityStats(regions[0], opts);
     }
+    async getSources(regions) {
+        const features = await (0, rxjs_1.firstValueFrom)(this.getFeaturesInMultipleRegions(regions).pipe((0, operators_1.toArray)()));
+        const sources = new Set();
+        for (const f of features) {
+            sources.add(f.get('source'));
+        }
+        return [...sources].map(source => ({
+            name: source,
+        }));
+    }
 }
 exports.BaseFeatureDataAdapter = BaseFeatureDataAdapter;

package/data_adapters/CytobandAdapter/CytobandAdapter.d.ts

@@ -1,6 +1,7 @@
 import { SimpleFeature } from '../../util';
 import { BaseAdapter } from '../BaseAdapter';
+import { BaseOptions } from '../BaseAdapter/BaseOptions';
 export default class CytobandAdapter extends BaseAdapter {
-    getData(): Promise<SimpleFeature[]>;
+    getData(opts?: BaseOptions): Promise<SimpleFeature[]>;
     freeResources(): void;
 }

package/data_adapters/CytobandAdapter/CytobandAdapter.js

@@ -1,20 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 // locals
 const util_1 = require("../../util");
 const io_1 = require("../../util/io");
 const BaseAdapter_1 = require("../BaseAdapter");
 class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
-    async getData() {
-        const pm = this.pluginManager;
-        const loc = this.getConf('cytobandLocation');
-        if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
+    async getData(opts) {
+        const conf = this.getConf('cytobandLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/cytoband.txt.gz') {
             return [];
         }
-        const buffer = await (0, io_1.openLocation)(loc, pm).readFile();
-        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
-        const text = new TextDecoder('utf8', { fatal: true }).decode(buf);
+        const pm = this.pluginManager;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(conf, pm), opts);
+        const decoder = new TextDecoder('utf8', { fatal: true });
+        const text = decoder.decode(buf);
         return text
             .split(/\n|\r\n|\r/)
             .filter(f => !!f.trim())
@@ -25,8 +24,9 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
                 refName: refName,
                 start: +start,
                 end: +end,
-                name: name,
-                type: type,
+                name,
+                type,
+                gieStain: type || name,
             });
         });
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.16.1",
+  "version": "2.17.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -44,7 +44,7 @@
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.0.0",
+    "dompurify": "^3.2.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "generic-filehandle": "^3.0.0",
@@ -72,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }