@jbrowse/core 2.2.2 → 2.3.0

package/util/index.d.ts

@@ -9,6 +9,7 @@ export * from './types';
 export * from './aborting';
 export * from './when';
 export * from './range';
+export * from './dedupe';
 export { SimpleFeature, isFeature };
 export * from './offscreenCanvasPonyfill';
 export * from './offscreenCanvasUtils';
@@ -340,4 +341,3 @@ export declare function measureGridWidth(elements: string[]): number;
 export declare function getEnv(obj: any): {
     pluginManager: PluginManager;
 };
-export declare function dedupe<T, U>(results: T[] | undefined, cb: (result: T) => U): T[];

package/util/index.js

@@ -30,7 +30,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
-exports.dedupe = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
+exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -46,6 +46,7 @@ __exportStar(require("./types"), exports);
 __exportStar(require("./aborting"), exports);
 __exportStar(require("./when"), exports);
 __exportStar(require("./range"), exports);
+__exportStar(require("./dedupe"), exports);
 __exportStar(require("./offscreenCanvasPonyfill"), exports);
 __exportStar(require("./offscreenCanvasUtils"), exports);
 exports.inDevelopment = typeof process === 'object' &&
@@ -1010,7 +1011,3 @@ function getEnv(obj) {
     return (0, mobx_state_tree_1.getEnv)(obj);
 }
 exports.getEnv = getEnv;
-function dedupe(results = [], cb) {
-    return results.filter((elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)));
-}
-exports.dedupe = dedupe;

package/util/offscreenCanvasUtils.js

@@ -37,7 +37,7 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
                         ? await (0, index_1.blobToDataURL)(await canvas.convertToBlob({
                             type: 'image/png',
                         }))
-                        : canvas.toDataURL() })),
+                        : canvas.toDataURL('image/png') })),
             };
         }
     }

package/util/stats.d.ts

@@ -26,12 +26,15 @@ export interface FeatureStats extends UnrectifiedFeatureStats {
  */
 export declare function calcStdFromSums(sum: number, sumSquares: number, n: number, population?: boolean): number;
 /**
- * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
- * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ * @param stats - a summary stats object with scoreSum, featureCount,
+ * scoreSumSquares, and basesCovered
+ * @returns - a summary stats object with
+ * scoreMean, scoreStdDev, and featureDensity added
  */
 export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
 /**
  * calculates per-base scores for variable width features over a region
+ *
  * @param region - object contains start, end
  * @param features - list of features with start, end, score
  * @returns array of numeric scores
@@ -39,9 +42,10 @@ export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
 export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Feature[]): number[];
 /**
  * transform a list of scores to summary statistics
+ *
  * @param region - object with start, end
  * @param features - array of features which are possibly summary features
  * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
-export declare function scoresToStats(region: NoAssemblyRegion, features: Observable<Feature>): Promise<FeatureStats>;
+export declare function scoresToStats(region: NoAssemblyRegion, feats: Observable<Feature>): Promise<FeatureStats>;
 export declare function blankStats(): FeatureStats;

package/util/stats.js

@@ -31,8 +31,10 @@ function calcStdFromSums(sum, sumSquares, n, population = false) {
 }
 exports.calcStdFromSums = calcStdFromSums;
 /**
- * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
- * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ * @param stats - a summary stats object with scoreSum, featureCount,
+ * scoreSumSquares, and basesCovered
+ * @returns - a summary stats object with
+ * scoreMean, scoreStdDev, and featureDensity added
  */
 function rectifyStats(s) {
     return {
@@ -45,6 +47,7 @@ function rectifyStats(s) {
 exports.rectifyStats = rectifyStats;
 /**
  * calculates per-base scores for variable width features over a region
+ *
  * @param region - object contains start, end
  * @param features - list of features with start, end, score
  * @returns array of numeric scores
@@ -78,39 +81,45 @@ function calcPerBaseStats(region, features) {
 exports.calcPerBaseStats = calcPerBaseStats;
 /**
  * transform a list of scores to summary statistics
+ *
  * @param region - object with start, end
  * @param features - array of features which are possibly summary features
  * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
-async function scoresToStats(region, features) {
+async function scoresToStats(region, feats) {
     const { start, end } = region;
-    const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await features
-        .pipe((0, operators_1.reduce)((seed, f) => {
-        const s = f.get('score');
-        const summary = f.get('summary');
-        const { scoreMax, scoreMin } = seed;
-        seed.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s);
-        seed.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s);
-        seed.scoreSum += s;
-        seed.scoreSumSquares += s * s;
-        seed.featureCount += 1;
-        return seed;
-    }, {
+    const seed = {
         scoreMin: Number.MAX_VALUE,
         scoreMax: Number.MIN_VALUE,
         scoreSum: 0,
         scoreSumSquares: 0,
         featureCount: 0,
-    }))
+    };
+    let found = false;
+    const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await feats
+        .pipe((0, operators_1.reduce)((acc, f) => {
+        const s = f.get('score');
+        const summary = f.get('summary');
+        const { scoreMax, scoreMin } = acc;
+        acc.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s);
+        acc.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s);
+        acc.scoreSum += s;
+        acc.scoreSumSquares += s * s;
+        acc.featureCount += 1;
+        found = true;
+        return acc;
+    }, seed))
         .toPromise();
-    return rectifyStats({
-        scoreMax,
-        scoreMin,
-        scoreSum,
-        scoreSumSquares,
-        featureCount,
-        basesCovered: end - start + 1,
-    });
+    return found
+        ? rectifyStats({
+            scoreMax,
+            scoreMin,
+            scoreSum,
+            scoreSumSquares,
+            featureCount,
+            basesCovered: end - start + 1,
+        })
+        : blankStats();
 }
 exports.scoresToStats = scoresToStats;
 function blankStats() {