@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/dist/util.js

@@ -1,4 +1,51 @@
 "use strict";
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
 var __read = (this && this.__read) || function (o, n) {
     var m = typeof Symbol === "function" && o[Symbol.iterator];
     if (!m) return o;
@@ -16,8 +63,14 @@ var __read = (this && this.__read) || function (o, n) {
     return ar;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNiceDomain = exports.getOrigin = exports.getScale = void 0;
+exports.round = exports.toP = exports.statsAutorun = exports.getStats = exports.groupBy = exports.getNiceDomain = exports.getOrigin = exports.getScale = exports.YSCALEBAR_LABEL_OFFSET = void 0;
 var d3_scale_1 = require("d3-scale");
+var mobx_1 = require("mobx");
+var util_1 = require("@jbrowse/core/util");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.YSCALEBAR_LABEL_OFFSET = 5;
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -144,4 +197,109 @@ function getNiceDomain(_a) {
     return scale.domain();
 }
 exports.getNiceDomain = getNiceDomain;
+function groupBy(array, predicate) {
+    return array.reduce(function (acc, value) {
+        var _a;
+        var entry = (acc[_a = predicate(value)] || (acc[_a] = []));
+        entry.push(value);
+        return acc;
+    }, {});
+}
+exports.groupBy = groupBy;
+function getStats(self, opts) {
+    return __awaiter(this, void 0, void 0, function () {
+        var rpcManager, nd, adapterConfig, autoscaleType, sessionId, params, results, scoreMin, scoreMean, scoreStdDev, _a, dynamicBlocks, bpPerPx, results, scoreMin, scoreMean, scoreStdDev;
+        return __generator(this, function (_b) {
+            switch (_b.label) {
+                case 0:
+                    rpcManager = (0, util_1.getSession)(self).rpcManager;
+                    nd = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
+                    adapterConfig = self.adapterConfig, autoscaleType = self.autoscaleType;
+                    sessionId = (0, tracks_1.getRpcSessionId)(self);
+                    params = __assign({ sessionId: sessionId, adapterConfig: adapterConfig, statusCallback: function (message) {
+                            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                                self.setMessage(message);
+                            }
+                        } }, opts);
+                    if (!(autoscaleType === 'global' || autoscaleType === 'globalsd')) return [3 /*break*/, 2];
+                    return [4 /*yield*/, rpcManager.call(sessionId, 'WiggleGetGlobalStats', params)];
+                case 1:
+                    results = (_b.sent());
+                    scoreMin = results.scoreMin, scoreMean = results.scoreMean, scoreStdDev = results.scoreStdDev;
+                    // globalsd uses heuristic to avoid unnecessary scoreMin<0
+                    // if the scoreMin is never less than 0
+                    // helps with most coverage bigwigs just being >0
+                    return [2 /*return*/, autoscaleType === 'globalsd'
+                            ? __assign(__assign({}, results), { scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev, scoreMax: scoreMean + nd * scoreStdDev }) : results];
+                case 2:
+                    if (!(autoscaleType === 'local' || autoscaleType === 'localsd')) return [3 /*break*/, 4];
+                    _a = (0, util_1.getContainingView)(self), dynamicBlocks = _a.dynamicBlocks, bpPerPx = _a.bpPerPx;
+                    return [4 /*yield*/, rpcManager.call(sessionId, 'WiggleGetMultiRegionStats', __assign(__assign({}, params), { regions: dynamicBlocks.contentBlocks.map(function (region) {
+                                var start = region.start, end = region.end;
+                                return __assign(__assign({}, JSON.parse(JSON.stringify(region))), { start: Math.floor(start), end: Math.ceil(end) });
+                            }), bpPerPx: bpPerPx }))];
+                case 3:
+                    results = (_b.sent());
+                    scoreMin = results.scoreMin, scoreMean = results.scoreMean, scoreStdDev = results.scoreStdDev;
+                    // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
+                    // scoreMin is never less than 0 helps with most coverage bigwigs
+                    // just being >0
+                    return [2 /*return*/, autoscaleType === 'localsd'
+                            ? __assign(__assign({}, results), { scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev, scoreMax: scoreMean + nd * scoreStdDev }) : results];
+                case 4:
+                    if (autoscaleType === 'zscale') {
+                        return [2 /*return*/, rpcManager.call(sessionId, 'WiggleGetGlobalStats', params)];
+                    }
+                    throw new Error("invalid autoscaleType '".concat(autoscaleType, "'"));
+            }
+        });
+    });
+}
+exports.getStats = getStats;
+function statsAutorun(self) {
+    var _this = this;
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function () { return __awaiter(_this, void 0, void 0, function () {
+        var aborter, view, statsRegion, wiggleStats, e_1;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 2, , 3]);
+                    aborter = new AbortController();
+                    view = (0, util_1.getContainingView)(self);
+                    self.setLoading(aborter);
+                    if (!view.initialized ||
+                        !self.estimatedStatsReady ||
+                        self.regionTooLarge) {
+                        return [2 /*return*/];
+                    }
+                    statsRegion = JSON.stringify(view.dynamicBlocks);
+                    return [4 /*yield*/, getStats(self, __assign({ signal: aborter.signal }, self.renderProps()))];
+                case 1:
+                    wiggleStats = _a.sent();
+                    if ((0, mobx_state_tree_1.isAlive)(self)) {
+                        self.updateStats(wiggleStats, statsRegion);
+                    }
+                    return [3 /*break*/, 3];
+                case 2:
+                    e_1 = _a.sent();
+                    if (!(0, util_1.isAbortException)(e_1) && (0, mobx_state_tree_1.isAlive)(self)) {
+                        console.error(e_1);
+                        self.setError(e_1);
+                    }
+                    return [3 /*break*/, 3];
+                case 3: return [2 /*return*/];
+            }
+        });
+    }); }, { delay: 1000 }));
+}
+exports.statsAutorun = statsAutorun;
+function toP(s) {
+    if (s === void 0) { s = 0; }
+    return +(+s).toPrecision(6);
+}
+exports.toP = toP;
+function round(value) {
+    return Math.round(value * 1e5) / 1e5;
+}
+exports.round = round;
 //# sourceMappingURL=util.js.map

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package/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -1,17 +1,18 @@
+import { BigWig } from '@gmod/bbi';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { Feature } from '@jbrowse/core/util';
 interface WiggleOptions extends BaseOptions {
     resolution?: number;
 }
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-    private bigwig;
+    private setupP?;
     static capabilities: string[];
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    private setup;
+    private setupPre;
+    setup(opts?: BaseOptions): Promise<{
+        bigwig: BigWig;
+        header: any;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<any>;
     getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").FeatureStats>;

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -3,32 +3,36 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { openLocation } from '@jbrowse/core/util/io';
 import { updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { map, mergeAll } from 'rxjs/operators';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { rectifyStats } from '@jbrowse/core/util/stats';
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        this.bigwig = new BigWig({
-            filehandle: openLocation(readConfObject(config, 'bigWigLocation'), this.pluginManager),
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const bigwig = new BigWig({
+            filehandle: openLocation(this.getConf('bigWigLocation'), this.pluginManager),
         });
+        const header = await updateStatus('Downloading bigwig header', statusCallback, () => bigwig.getHeader(opts));
+        return { bigwig, header };
     }
     async setup(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return updateStatus('Downloading bigwig header', statusCallback, () => this.bigwig.getHeader(opts));
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
     }
     async getRefNames(opts) {
-        const { refsByName } = await this.setup(opts);
+        const { header: { refsByName }, } = await this.setup(opts);
         return Object.keys(refsByName);
     }
     async refIdToName(refId) {
         var _a;
-        const { refsByNumber } = await this.setup();
+        const { header: { refsByNumber }, } = await this.setup();
         return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
     }
     async getGlobalStats(opts) {
-        const { totalSummary } = await this.setup(opts);
+        const { header: { totalSummary }, } = await this.setup(opts);
         return rectifyStats(totalSummary);
     }
     getFeatures(region, opts = {}) {
@@ -36,16 +40,31 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
         const { bpPerPx = 0, signal, resolution = 1, statusCallback = () => { }, } = opts;
         return ObservableCreate(async (observer) => {
             statusCallback('Downloading bigwig data');
-            const ob = await this.bigwig.getFeatureStream(refName, start, end, {
+            const source = this.getConf('source');
+            const { bigwig } = await this.setup(opts);
+            const feats = await bigwig.getFeatures(refName, start, end, {
                 ...opts,
                 basesPerSpan: bpPerPx / resolution,
             });
-            ob.pipe(mergeAll(), map(record => {
-                return new SimpleFeature({
-                    id: `${refName}:${record.start}-${record.end}`,
-                    data: { ...record, refName },
+            for (let i = 0; i < feats.length; i++) {
+                const data = feats[i];
+                if (source) {
+                    // @ts-ignore
+                    data.source = source;
+                }
+                const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`;
+                // @ts-ignore
+                data.refName = refName;
+                data.uniqueId = uniqueId;
+                observer.next({
+                    // @ts-ignore
+                    get: (str) => data[str],
+                    id: () => uniqueId,
+                    // @ts-ignore
+                    toJSON: () => data,
                 });
-            })).subscribe(observer);
+            }
+            observer.complete();
         }, signal);
     }
     // always render bigwig instead of calculating a feature density for it

package/esm/BigWigAdapter/BigWigAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigWigAdapter.js","sourceRoot":"","sources":["../../src/BigWigAdapter/BigWigAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAClC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,YAAY,EAA2B,MAAM,0BAA0B,CAAA;AAMhF,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAUvD,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;YACxB,UAAU,EAAE,YAAY,CACtB,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAC9B,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,YAAY,CAC/B,2BAA2B,EAC3B,cAAc,EACd,GAAG,EAAE,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAC7B,CAAA;QACD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IAC3B,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EACJ,MAAM,EAAE,EAAE,UAAU,EAAE,GACvB,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,OAAO,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAChC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,KAAa;;QACpC,MAAM,EACJ,MAAM,EAAE,EAAE,YAAY,EAAE,GACzB,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtB,OAAO,MAAA,YAAY,CAAC,KAAK,CAAC,0CAAE,IAAI,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,cAAc,CAAC,IAAkB;QAC5C,MAAM,EACJ,MAAM,EAAE,EAAE,YAAY,EAAE,GACzB,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,OAAO,YAAY,CAAC,YAAuC,CAAC,CAAA;IAC9D,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAsB,EAAE;QACzD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EACJ,OAAO,GAAG,CAAC,EACX,MAAM,EACN,UAAU,GAAG,CAAC,EACd,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,GAC1B,GAAG,IAAI,CAAA;QACR,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,cAAc,CAAC,yBAAyB,CAAC,CAAA;YACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;YACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACzC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBAC1D,GAAG,IAAI;gBACP,YAAY,EAAE,OAAO,GAAG,UAAU;aACnC,CAAC,CAAA;YAEF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,MAAM,EAAE;oBACV,aAAa;oBACb,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;iBACrB;gBACD,MAAM,QAAQ,GAAG,GAAG,MAAM,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;gBACxE,aAAa;gBACb,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;gBACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC;oBACZ,aAAa;oBACb,GAAG,EAAE,CAAC,GAAW,EAAE,EAAE,CAAE,IAAgC,CAAC,GAAG,CAAC;oBAC5D,EAAE,EAAE,GAAG,EAAE,CAAC,QAAQ;oBAClB,aAAa;oBACb,MAAM,EAAE,GAAG,EAAE,CAAC,IAAI;iBACnB,CAAC,CAAA;aACH;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,uEAAuE;IACvE,KAAK,CAAC,oBAAoB,CAAC,QAAkB;QAC3C,OAAO,EAAE,cAAc,EAAE,CAAC,EAAE,CAAA;IAC9B,CAAC;IAEM,aAAa,KAAU,CAAC;;AAjGjB,0BAAY,GAAG;IAC3B,eAAe;IACf,eAAe;IACf,gBAAgB;CACjB,CAAA"}

package/esm/BigWigAdapter/configSchema.js

@@ -7,5 +7,10 @@ export default ConfigurationSchema('BigWigAdapter', {
             locationType: 'UriLocation',
         },
     },
+    source: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Used for multiwiggle',
+    },
 }, { explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/esm/BigWigAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,sBAAsB;KACpC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/BigWigAdapter/index.d.ts

@@ -1 +1,3 @@
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/BigWigAdapter/index.js

@@ -1,2 +1,15 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BigWigAdapter',
+        configSchema,
+        adapterCapabilities: [
+            'hasResolution',
+            'hasLocalStats',
+            'hasGlobalStats',
+        ],
+        getAdapterClass: () => import('./BigWigAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/BigWigAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigWigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigWigAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY;QACZ,mBAAmB,EAAE;YACnB,eAAe;YACf,eAAe;YACf,gBAAgB;SACjB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const ConfirmDialog: ({ tracks, onClose, }: {
+    tracks: AnyConfigurationModel[];
+    onClose: (arg: boolean, arg1?: {
+        name: string;
+    }) => void;
+}) => JSX.Element;
+export default ConfirmDialog;

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js

@@ -0,0 +1,26 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogActions, DialogContent, DialogTitle, TextField, Typography, } from '@mui/material';
+import { readConfObject, } from '@jbrowse/core/configuration';
+const ConfirmDialog = ({ tracks, onClose, }) => {
+    const [val, setVal] = useState('MultiWiggle ' + Date.now());
+    const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');
+    return (React.createElement(Dialog, { open: true, onClose: () => onClose(false) },
+        React.createElement(DialogTitle, null, "Confirm multi-wiggle track create"),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null,
+                !allQuant
+                    ? 'Not every track looks like a QuantitativeTrack. This could have unexpected behavior, confirm if it looks ok.'
+                    : null,
+                "Listing:"),
+            React.createElement("ul", null, tracks.map(track => (React.createElement("li", { key: track.trackId },
+                readConfObject(track, 'name'),
+                " - ",
+                track.type)))),
+            React.createElement(TextField, { value: val, onChange: event => setVal(event.target.value), helperText: "Track name" }),
+            React.createElement(Typography, null, "Confirm creation of track?")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => onClose(false), color: "primary" }, "Cancel"),
+            React.createElement(Button, { onClick: () => onClose(true, { name: val }), color: "primary", variant: "contained", autoFocus: true }, "Submit"))));
+};
+export default ConfirmDialog;
+//# sourceMappingURL=ConfirmDialog.js.map

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ConfirmDialog.js","sourceRoot":"","sources":["../../src/CreateMultiWiggleExtension/ConfirmDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AAEpC,MAAM,aAAa,GAAG,CAAC,EACrB,MAAM,EACN,OAAO,GAIR,EAAE,EAAE;IACH,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;IAC3D,MAAM,QAAQ,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,mBAAmB,CAAC,CAAA;IAClE,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;QACxC,oBAAC,WAAW,4CAAgD;QAC5D,oBAAC,aAAa;YACZ,oBAAC,UAAU;gBACR,CAAC,QAAQ;oBACR,CAAC,CAAC,8GAA8G;oBAChH,CAAC,CAAC,IAAI;2BAEG;YACb,gCACG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACnB,4BAAI,GAAG,EAAE,KAAK,CAAC,OAAO;gBACnB,cAAc,CAAC,KAAK,EAAE,MAAM,CAAC;;gBAAK,KAAK,CAAC,IAAI,CAC1C,CACN,CAAC,CACC;YACL,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,UAAU,EAAC,YAAY,GACvB;YACF,oBAAC,UAAU,qCAAwC,CACrC;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAC,SAAS,aAE7C;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EAC3C,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,SAAS,mBAGF,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAA;AAED,eAAe,aAAa,CAAA"}

package/esm/CreateMultiWiggleExtension/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pm: PluginManager): void;

package/esm/CreateMultiWiggleExtension/index.js

@@ -0,0 +1,51 @@
+import { lazy } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+const ConfirmDialog = lazy(() => import('./ConfirmDialog'));
+export default function (pm) {
+    pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', () => {
+        return [
+            {
+                label: 'Create multi-wiggle track',
+                onClick: (model) => {
+                    const tracks = model.selection;
+                    const trackIds = tracks.map(c => readConfObject(c, 'name'));
+                    function makeTrack(arg) {
+                        const subadapters = tracks
+                            .map(c => readConfObject(c, 'adapter'))
+                            .map((c, idx) => ({ ...c, source: trackIds[idx] }));
+                        const assemblyNames = [
+                            ...new Set(tracks.map(c => readConfObject(c, 'assemblyNames')).flat()),
+                        ];
+                        const now = +Date.now();
+                        const trackId = `multitrack-${now}-sessionTrack`;
+                        getSession(model).addTrackConf({
+                            type: 'MultiQuantitativeTrack',
+                            trackId,
+                            name: arg.name,
+                            assemblyNames,
+                            adapter: {
+                                type: 'MultiWiggleAdapter',
+                                subadapters,
+                            },
+                        });
+                        model.view.showTrack(trackId);
+                    }
+                    getSession(model).queueDialog(handleClose => [
+                        ConfirmDialog,
+                        {
+                            tracks,
+                            onClose: (arg, arg1) => {
+                                if (arg) {
+                                    makeTrack(arg1);
+                                }
+                                handleClose();
+                            },
+                        },
+                    ]);
+                },
+            },
+        ];
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/CreateMultiWiggleExtension/index.js.map

@@ -0,0 +1 @@
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package/esm/DensityRenderer/DensityRenderer.d.ts

@@ -0,0 +1,6 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
+        reducedFeatures: import("@jbrowse/core/util").Feature[];
+    }>;
+}

package/esm/DensityRenderer/DensityRenderer.js

@@ -0,0 +1,8 @@
+import { drawDensity } from '../drawxy';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    async draw(ctx, props) {
+        return drawDensity(ctx, props);
+    }
+}
+//# sourceMappingURL=DensityRenderer.js.map

package/esm/DensityRenderer/DensityRenderer.js.map

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package/esm/DensityRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/DensityRenderer/configSchema.js

@@ -0,0 +1,5 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+const configSchema = ConfigurationSchema('DensityRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/DensityRenderer/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/DensityRenderer/index.d.ts

@@ -1,6 +1,3 @@
-import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
-export { default as ReactComponent } from '../WiggleRendering';
-export default class DensityRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
-}
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/DensityRenderer/index.js

@@ -1,39 +1,12 @@
-import { readConfObject, ConfigurationSchema, } from '@jbrowse/core/configuration';
-import { featureSpanPx } from '@jbrowse/core/util';
-import { getScale } from '../util';
-import ConfigSchema from '../configSchema';
-import WiggleBaseRenderer from '../WiggleBaseRenderer';
-export { default as ReactComponent } from '../WiggleRendering';
-export default class DensityRenderer extends WiggleBaseRenderer {
-    async draw(ctx, props) {
-        const { features, regions, bpPerPx, scaleOpts, height, config } = props;
-        const [region] = regions;
-        const pivot = readConfObject(config, 'bicolorPivot');
-        const pivotValue = readConfObject(config, 'bicolorPivotValue');
-        const negColor = readConfObject(config, 'negColor');
-        const posColor = readConfObject(config, 'posColor');
-        const color = readConfObject(config, 'color');
-        let colorCallback;
-        if (color === '#f0f') {
-            const colorScale = pivot !== 'none'
-                ? getScale({
-                    ...scaleOpts,
-                    pivotValue,
-                    range: [negColor, 'white', posColor],
-                })
-                : getScale({ ...scaleOpts, range: ['white', posColor] });
-            colorCallback = (feature) => colorScale(feature.get('score'));
-        }
-        else {
-            colorCallback = (feature) => readConfObject(config, 'color', { feature });
-        }
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            const w = rightPx - leftPx + 0.3; // fudge factor for subpixel rendering
-            ctx.fillStyle = colorCallback(feature);
-            ctx.fillRect(leftPx, 0, w, height);
-        }
-    }
-}
-export const configSchema = ConfigurationSchema('DensityRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+import configSchema from './configSchema';
+import DensityRenderer from './DensityRenderer';
+import ReactComponent from '../WiggleRendering';
+export default (pluginManager) => {
+    pluginManager.addRendererType(() => new DensityRenderer({
+        name: 'DensityRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/DensityRenderer/index.js.map

@@ -1 +1 @@
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package/esm/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -1,4 +1,6 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
-    draw(ctx: any, props: any): Promise<void>;
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
+        reducedFeatures: import("@jbrowse/core/util").Feature[];
+    }>;
 }
-import WiggleBaseRenderer from "../WiggleBaseRenderer";