@jbrowse/core 2.3.2 → 2.3.3

package/ui/FatalErrorDialog.js

@@ -36,7 +36,6 @@ const ResetComponent = ({ onFactoryReset, resetButtonText, }) => {
         react_1.default.createElement(FactoryResetDialog_1.default, { onClose: () => setDialogOpen(false), open: dialogOpen, onFactoryReset: onFactoryReset })));
 };
 const FatalErrorDialog = ({ componentStack, error = 'No error message provided', onFactoryReset, resetButtonText = 'Factory Reset', }) => {
-    console.error(error);
     return (react_1.default.createElement(material_1.Dialog, { open: true },
         react_1.default.createElement(material_1.DialogTitle, { style: { background: '#e88' } }, "Fatal error"),
         react_1.default.createElement(material_1.DialogContent, null,

package/util/Base1DUtils.d.ts

@@ -30,3 +30,9 @@ export declare function bpToPx({ refName, coord, regionNumber, self, }: {
     index: number;
     offsetPx: number;
 } | undefined;
+export declare function bpToPxMap({ refName, coord, regionNumber, self, }: {
+    refName: string;
+    coord: number;
+    regionNumber?: number;
+    self: ViewSnap;
+}): {};

package/util/Base1DUtils.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.bpToPx = exports.pxToBp = exports.moveTo = void 0;
+exports.bpToPxMap = exports.bpToPx = exports.pxToBp = exports.moveTo = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 function lengthBetween(self, start, end) {
     let bpSoFar = 0;
@@ -57,6 +57,9 @@ function moveTo(self, start, end) {
     self.scrollTo(Math.round(bpToStart / self.bpPerPx));
 }
 exports.moveTo = moveTo;
+function coord(r, bp) {
+    return Math.floor(r.reversed ? r.end - bp : r.start + bp) + 1;
+}
 // manual return type since getSnapshot hard to infer here
 function pxToBp(self, px) {
     var _a;
@@ -65,16 +68,14 @@ function pxToBp(self, px) {
     const blocks = staticBlocks.contentBlocks;
     const bp = (offsetPx + px) * bpPerPx;
     if (bp < 0) {
-        const region = displayedRegions[0];
-        const snap = (0, mobx_state_tree_1.getSnapshot)(region);
+        const r = displayedRegions[0];
+        const snap = (0, mobx_state_tree_1.getSnapshot)(r);
         // @ts-ignore
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
             oob: true,
-            coord: region.reversed
-                ? Math.floor(region.end - bp) + 1
-                : Math.floor(region.start + bp) + 1,
+            coord: coord(r, bp),
             offset: bp,
             index: 0,
         };
@@ -82,20 +83,18 @@ function pxToBp(self, px) {
     const interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
     let currBlock = 0;
     for (let i = 0; i < displayedRegions.length; i++) {
-        const region = displayedRegions[i];
-        const len = region.end - region.start;
+        const r = displayedRegions[i];
+        const len = r.end - r.start;
         const offset = bp - bpSoFar;
         if (len + bpSoFar > bp && bpSoFar <= bp) {
-            const snap = (0, mobx_state_tree_1.getSnapshot)(region);
+            const snap = (0, mobx_state_tree_1.getSnapshot)(r);
             // @ts-ignore
             return {
                 // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
                 ...snap,
                 oob: false,
                 offset,
-                coord: region.reversed
-                    ? Math.floor(region.end - offset) + 1
-                    : Math.floor(region.start + offset) + 1,
+                coord: coord(r, offset),
                 index: i,
             };
         }
@@ -110,19 +109,17 @@ function pxToBp(self, px) {
         }
     }
     if (bp >= bpSoFar && displayedRegions.length) {
-        const region = displayedRegions[displayedRegions.length - 1];
-        const len = region.end - region.start;
+        const r = displayedRegions[displayedRegions.length - 1];
+        const len = r.end - r.start;
         const offset = bp - bpSoFar + len;
-        const snap = (0, mobx_state_tree_1.getSnapshot)(region);
+        const snap = (0, mobx_state_tree_1.getSnapshot)(r);
         // @ts-ignore
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
             oob: true,
             offset,
-            coord: region.reversed
-                ? Math.floor(region.end - offset) + 1
-                : Math.floor(region.start + offset) + 1,
+            coord: coord(r, offset),
             index: displayedRegions.length - 1,
         };
     }
@@ -148,13 +145,11 @@ function bpToPx({ refName, coord, regionNumber, self, }) {
     let currBlock = 0;
     let i = 0;
     for (; i < displayedRegions.length; i++) {
-        const region = displayedRegions[i];
-        const len = region.end - region.start;
-        if (refName === region.refName &&
-            coord >= region.start &&
-            coord <= region.end) {
+        const r = displayedRegions[i];
+        const len = r.end - r.start;
+        if (refName === r.refName && coord >= r.start && coord <= r.end) {
             if (regionNumber ? regionNumber === i : true) {
-                bpSoFar += region.reversed ? region.end - coord : coord - region.start;
+                bpSoFar += r.reversed ? r.end - coord : coord - r.start;
                 break;
             }
         }
@@ -178,3 +173,41 @@ function bpToPx({ refName, coord, regionNumber, self, }) {
     return undefined;
 }
 exports.bpToPx = bpToPx;
+function bpToPxMap({ refName, coord, regionNumber, self, }) {
+    var _a;
+    let bpSoFar = 0;
+    const { interRegionPaddingWidth, bpPerPx, displayedRegions, staticBlocks } = self;
+    const blocks = staticBlocks.contentBlocks;
+    const interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
+    const map = {};
+    let currBlock = 0;
+    let i = 0;
+    for (; i < displayedRegions.length; i++) {
+        const r = displayedRegions[i];
+        const len = r.end - r.start;
+        if (refName === r.refName && coord >= r.start && coord <= r.end) {
+            if (regionNumber !== undefined ? regionNumber === i : true) {
+                bpSoFar += r.reversed ? r.end - coord : coord - r.start;
+                break;
+            }
+        }
+        // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
+        // a static block
+        if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
+            bpSoFar += len + interRegionPaddingBp;
+            currBlock++;
+        }
+        else {
+            bpSoFar += len;
+        }
+    }
+    const found = displayedRegions[i];
+    if (found) {
+        return {
+            index: i,
+            offsetPx: Math.round(bpSoFar / bpPerPx),
+        };
+    }
+    return map;
+}
+exports.bpToPxMap = bpToPxMap;

package/util/Base1DViewModel.d.ts

@@ -78,7 +78,9 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
      */
     pxToBp(px: number): {
         coord: number;
-        index: number;
+        index: number; /**
+         * #getter
+         */
         refName: string;
         oob: boolean;
         assemblyName: string;

package/util/index.d.ts

@@ -342,3 +342,7 @@ export declare function getEnv(obj: any): {
     pluginManager: PluginManager;
 };
 export declare function localStorageGetItem(item: string): string | null | undefined;
+export declare function max(arr: number[]): number;
+export declare function min(arr: number[]): number;
+export declare function sum(arr: number[]): number;
+export declare function avg(arr: number[]): number;

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.localStorageGetItem = 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.avg = exports.sum = exports.min = exports.max = exports.localStorageGetItem = 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"));
@@ -66,7 +66,7 @@ function useDebounce(value, delay) {
     return debouncedValue;
 }
 exports.useDebounce = useDebounce;
-// https://stackoverflow.com/questions/56283920/how-to-debounce-a-callback-in-functional-component-using-hooks
+// https://stackoverflow.com/questions/56283920/
 function useDebouncedCallback(callback, wait = 400) {
     // track args & timeout handle between calls
     const argsRef = (0, react_1.useRef)();
@@ -1004,7 +1004,7 @@ function getStr(obj) {
 exports.getStr = getStr;
 // heuristic measurement for a column of a @mui/x-data-grid, pass in values from a column
 function measureGridWidth(elements) {
-    return Math.max(...elements.map(element => Math.min(Math.max(measureText(getStr(element), 14) + 50, 80), 1000)));
+    return max(elements.map(element => Math.min(Math.max(measureText(getStr(element), 14) + 50, 80), 1000)));
 }
 exports.measureGridWidth = measureGridWidth;
 function getEnv(obj) {
@@ -1017,3 +1017,31 @@ function localStorageGetItem(item) {
         : undefined;
 }
 exports.localStorageGetItem = localStorageGetItem;
+function max(arr) {
+    let max = -Infinity;
+    for (let i = 0; i < arr.length; i++) {
+        max = arr[i] > max ? arr[i] : max;
+    }
+    return max;
+}
+exports.max = max;
+function min(arr) {
+    let min = Infinity;
+    for (let i = 0; i < arr.length; i++) {
+        min = arr[i] < min ? arr[i] : min;
+    }
+    return min;
+}
+exports.min = min;
+function sum(arr) {
+    let sum = 0;
+    for (let i = 0; i < arr.length; i++) {
+        sum += arr[i];
+    }
+    return sum;
+}
+exports.sum = sum;
+function avg(arr) {
+    return sum(arr) / arr.length;
+}
+exports.avg = avg;

package/util/stats.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.blankStats = exports.scoresToStats = exports.calcPerBaseStats = exports.rectifyStats = exports.calcStdFromSums = void 0;
+const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 /**
  * calculate standard deviation using the 'shortcut method' that accepts
@@ -96,8 +97,7 @@ async function scoresToStats(region, feats) {
         featureCount: 0,
     };
     let found = false;
-    const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await feats
-        .pipe((0, operators_1.reduce)((acc, f) => {
+    const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await (0, rxjs_1.firstValueFrom)(feats.pipe((0, operators_1.reduce)((acc, f) => {
         const s = f.get('score');
         const summary = f.get('summary');
         const { scoreMax, scoreMin } = acc;
@@ -108,8 +108,7 @@ async function scoresToStats(region, feats) {
         acc.featureCount += 1;
         found = true;
         return acc;
-    }, seed))
-        .toPromise();
+    }, seed)));
     return found
         ? rectifyStats({
             scoreMax,