@jbrowse/core 2.2.1 → 2.3.0

package/ui/ViewLauncher.js

@@ -0,0 +1,50 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+// locals
+const util_1 = require("../util");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    selectPaper: {
+        padding: theme.spacing(4),
+    },
+}));
+const ViewLauncher = (0, mobx_react_1.observer)(({ session }) => {
+    var _a;
+    const { classes } = useStyles();
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const viewTypes = pluginManager.getElementTypeRecord('view').all();
+    const [value, setValue] = (0, react_1.useState)((_a = viewTypes[0]) === null || _a === void 0 ? void 0 : _a.name);
+    return (react_1.default.createElement(material_1.Paper, { className: classes.selectPaper },
+        react_1.default.createElement(material_1.Typography, null, "Select a view to launch"),
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ displayName, name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName))))),
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Button, { onClick: () => session.addView(value, {}), variant: "contained", color: "primary" }, "Launch view"))));
+});
+exports.default = ViewLauncher;

package/ui/index.d.ts

@@ -1,18 +1,19 @@
 export * from './theme';
 export { LogoFull, Logomark } from './Logo';
 export { default as App } from './App';
-export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
-export { default as ErrorMessage } from './ErrorMessage';
 export { default as AssemblySelector } from './AssemblySelector';
-export { default as FileSelector } from './FileSelector';
-export { default as PrerenderedCanvas } from './PrerenderedCanvas';
-export { default as ResizeHandle } from './ResizeHandle';
+export { default as CascadingMenu } from './CascadingMenu';
+export { default as Dialog } from './Dialog';
 export { default as EditableTypography } from './EditableTypography';
+export { default as ErrorMessage } from './ErrorMessage';
 export { default as FactoryResetDialog } from './FactoryResetDialog';
-export { default as Tooltip } from './Tooltip';
 export { default as FatalErrorDialog } from './FatalErrorDialog';
+export { default as FileSelector } from './FileSelector';
+export { default as LoadingEllipses } from './LoadingEllipses';
 export { default as Menu } from './Menu';
-export { default as CascadingMenu } from './CascadingMenu';
+export { default as PrerenderedCanvas } from './PrerenderedCanvas';
+export { default as Tooltip } from './Tooltip';
+export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
+export { default as ResizeHandle } from './ResizeHandle';
 export { default as SanitizedHTML } from './SanitizedHTML';
-export { default as LoadingEllipses } from './LoadingEllipses';
 export * from './Menu';

package/ui/index.js

@@ -17,39 +17,41 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LoadingEllipses = exports.SanitizedHTML = exports.CascadingMenu = exports.Menu = exports.FatalErrorDialog = exports.Tooltip = exports.FactoryResetDialog = exports.EditableTypography = exports.ResizeHandle = exports.PrerenderedCanvas = exports.FileSelector = exports.AssemblySelector = exports.ErrorMessage = exports.ReturnToImportFormDialog = exports.App = exports.Logomark = exports.LogoFull = void 0;
+exports.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.Tooltip = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.App = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
 Object.defineProperty(exports, "Logomark", { enumerable: true, get: function () { return Logo_1.Logomark; } });
 var App_1 = require("./App");
 Object.defineProperty(exports, "App", { enumerable: true, get: function () { return __importDefault(App_1).default; } });
-var ReturnToImportFormDialog_1 = require("./ReturnToImportFormDialog");
-Object.defineProperty(exports, "ReturnToImportFormDialog", { enumerable: true, get: function () { return __importDefault(ReturnToImportFormDialog_1).default; } });
-var ErrorMessage_1 = require("./ErrorMessage");
-Object.defineProperty(exports, "ErrorMessage", { enumerable: true, get: function () { return __importDefault(ErrorMessage_1).default; } });
 var AssemblySelector_1 = require("./AssemblySelector");
 Object.defineProperty(exports, "AssemblySelector", { enumerable: true, get: function () { return __importDefault(AssemblySelector_1).default; } });
-var FileSelector_1 = require("./FileSelector");
-Object.defineProperty(exports, "FileSelector", { enumerable: true, get: function () { return __importDefault(FileSelector_1).default; } });
-var PrerenderedCanvas_1 = require("./PrerenderedCanvas");
-Object.defineProperty(exports, "PrerenderedCanvas", { enumerable: true, get: function () { return __importDefault(PrerenderedCanvas_1).default; } });
-var ResizeHandle_1 = require("./ResizeHandle");
-Object.defineProperty(exports, "ResizeHandle", { enumerable: true, get: function () { return __importDefault(ResizeHandle_1).default; } });
+var CascadingMenu_1 = require("./CascadingMenu");
+Object.defineProperty(exports, "CascadingMenu", { enumerable: true, get: function () { return __importDefault(CascadingMenu_1).default; } });
+var Dialog_1 = require("./Dialog");
+Object.defineProperty(exports, "Dialog", { enumerable: true, get: function () { return __importDefault(Dialog_1).default; } });
 var EditableTypography_1 = require("./EditableTypography");
 Object.defineProperty(exports, "EditableTypography", { enumerable: true, get: function () { return __importDefault(EditableTypography_1).default; } });
+var ErrorMessage_1 = require("./ErrorMessage");
+Object.defineProperty(exports, "ErrorMessage", { enumerable: true, get: function () { return __importDefault(ErrorMessage_1).default; } });
 var FactoryResetDialog_1 = require("./FactoryResetDialog");
 Object.defineProperty(exports, "FactoryResetDialog", { enumerable: true, get: function () { return __importDefault(FactoryResetDialog_1).default; } });
-var Tooltip_1 = require("./Tooltip");
-Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
 var FatalErrorDialog_1 = require("./FatalErrorDialog");
 Object.defineProperty(exports, "FatalErrorDialog", { enumerable: true, get: function () { return __importDefault(FatalErrorDialog_1).default; } });
+var FileSelector_1 = require("./FileSelector");
+Object.defineProperty(exports, "FileSelector", { enumerable: true, get: function () { return __importDefault(FileSelector_1).default; } });
+var LoadingEllipses_1 = require("./LoadingEllipses");
+Object.defineProperty(exports, "LoadingEllipses", { enumerable: true, get: function () { return __importDefault(LoadingEllipses_1).default; } });
 var Menu_1 = require("./Menu");
 Object.defineProperty(exports, "Menu", { enumerable: true, get: function () { return __importDefault(Menu_1).default; } });
-var CascadingMenu_1 = require("./CascadingMenu");
-Object.defineProperty(exports, "CascadingMenu", { enumerable: true, get: function () { return __importDefault(CascadingMenu_1).default; } });
+var PrerenderedCanvas_1 = require("./PrerenderedCanvas");
+Object.defineProperty(exports, "PrerenderedCanvas", { enumerable: true, get: function () { return __importDefault(PrerenderedCanvas_1).default; } });
+var Tooltip_1 = require("./Tooltip");
+Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
+var ReturnToImportFormDialog_1 = require("./ReturnToImportFormDialog");
+Object.defineProperty(exports, "ReturnToImportFormDialog", { enumerable: true, get: function () { return __importDefault(ReturnToImportFormDialog_1).default; } });
+var ResizeHandle_1 = require("./ResizeHandle");
+Object.defineProperty(exports, "ResizeHandle", { enumerable: true, get: function () { return __importDefault(ResizeHandle_1).default; } });
 var SanitizedHTML_1 = require("./SanitizedHTML");
 Object.defineProperty(exports, "SanitizedHTML", { enumerable: true, get: function () { return __importDefault(SanitizedHTML_1).default; } });
-var LoadingEllipses_1 = require("./LoadingEllipses");
-Object.defineProperty(exports, "LoadingEllipses", { enumerable: true, get: function () { return __importDefault(LoadingEllipses_1).default; } });
 __exportStar(require("./Menu"), exports);

package/util/Base1DUtils.js

@@ -109,7 +109,7 @@ function pxToBp(self, px) {
             bpSoFar += len;
         }
     }
-    if (bp >= bpSoFar) {
+    if (bp >= bpSoFar && displayedRegions.length) {
         const region = displayedRegions[displayedRegions.length - 1];
         const len = region.end - region.start;
         const offset = bp - bpSoFar + len;

package/util/analytics.js

@@ -89,7 +89,10 @@ exports.writeGAAnalytics = writeGAAnalytics;
 function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {
     if (rootModel &&
         !(0, configuration_1.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
+        // ok if these are unhandled
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeGAAnalytics(rootModel, initialTimestamp);
     }
 }

package/util/dedupe.d.ts

@@ -0,0 +1,3 @@
+type Hasher<T> = (input: T) => string;
+export declare function dedupe<T>(list: T[], hasher?: Hasher<T>): T[];
+export {};

package/util/dedupe.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.dedupe = void 0;
+// from https://github.com/seriousManual/dedupe/blob/master/LICENSE
+function dedupe(list, hasher = JSON.stringify) {
+    const clone = [];
+    const lookup = new Set();
+    for (let i = 0; i < list.length; i++) {
+        const entry = list[i];
+        const hashed = hasher(entry);
+        if (!lookup.has(hashed)) {
+            clone.push(entry);
+            lookup.add(hashed);
+        }
+    }
+    return clone;
+}
+exports.dedupe = dedupe;

package/util/formatFastaStrings.d.ts

@@ -7,7 +7,7 @@ export interface SeqChunk {
  * ref https://stackoverflow.com/a/51506718/2129219
  *
  * @param seqString -  string
- * @returns formated sequence string
+ * @returns formatted sequence string
  */
 export declare function formatFastaLines(seqString: string): string;
 /**

package/util/formatFastaStrings.js

@@ -6,7 +6,7 @@ exports.formatSeqFasta = exports.formatFastaLines = void 0;
  * ref https://stackoverflow.com/a/51506718/2129219
  *
  * @param seqString -  string
- * @returns formated sequence string
+ * @returns formatted sequence string
  */
 function formatFastaLines(seqString) {
     return seqString.replace(/(.{1,80})/g, '$1\n').trimEnd();

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';

package/util/index.js

@@ -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' &&

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() {

package/util/tracks.d.ts

@@ -31,7 +31,7 @@ export declare function storeBlobLocation(location: PreFileLocation): import("./
  * creates a new location from the provided location including the appropriate suffix and location type
  * @param location - the FileLocation
  * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided prameters
+ * @returns the constructed location object from the provided parameters
  */
 export declare function makeIndex(location: FileLocation, suffix: string): import("./types").BlobLocation | {
     uri: string;

package/util/tracks.js

@@ -87,7 +87,7 @@ exports.storeBlobLocation = storeBlobLocation;
  * creates a new location from the provided location including the appropriate suffix and location type
  * @param location - the FileLocation
  * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided prameters
+ * @returns the constructed location object from the provided parameters
  */
 function makeIndex(location, suffix) {
     if ('uri' in location) {