@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/esm/index.js

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+import Plugin from '@jbrowse/core/Plugin';
+import { getFileName, } from '@jbrowse/core/util/tracks';
+// locals
+import WiggleBaseRenderer from './WiggleBaseRenderer';
+import WiggleRendering from './WiggleRendering';
+import BigWigAdapterF from './BigWigAdapter';
+import QuantitativeTrackF from './QuantitativeTrack';
+import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
+import MultiWiggleAdapterF from './MultiWiggleAdapter';
+import DensityRendererF from './DensityRenderer';
+import XYPlotRendererF from './XYPlotRenderer';
+import LinePlotRendererF from './LinePlotRenderer';
+import LinearWiggleDisplayF from './LinearWiggleDisplay';
+import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay';
+import MultiXYPlotRendererF from './MultiXYPlotRenderer';
+import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer';
+import MultiDensityRendererF from './MultiDensityRenderer';
+import MultiLineRendererF from './MultiLineRenderer';
+import MultiRowLineRendererF from './MultiRowLineRenderer';
+import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
+import MultiWiggleAddTrackWidgetF from './MultiWiggleAddTrackWidget';
+import * as utils from './util';
+import { WiggleGetGlobalStats, WiggleGetMultiRegionStats, MultiWiggleGetSources, } from './WiggleRPC/rpcMethods';
+import { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, Tooltip, } from './LinearWiggleDisplay';
+import { ReactComponent as XYPlotRendererReactComponent, configSchema as xyPlotRendererConfigSchema, XYPlotRenderer, } from './XYPlotRenderer';
+export default class WigglePlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'WigglePlugin';
+        this.exports = {
+            LinearWiggleDisplayReactComponent,
+            XYPlotRendererReactComponent,
+            XYPlotRenderer,
+            WiggleBaseRenderer,
+            xyPlotRendererConfigSchema,
+            utils,
+            linearWiggleDisplayModelFactory,
+        };
+    }
+    install(pm) {
+        MultiWiggleAdapterF(pm);
+        BigWigAdapterF(pm);
+        QuantitativeTrackF(pm);
+        MultiQuantitativeTrackF(pm);
+        LinearWiggleDisplayF(pm);
+        MultiLinearWiggleDisplayF(pm);
+        LinePlotRendererF(pm);
+        XYPlotRendererF(pm);
+        DensityRendererF(pm);
+        MultiXYPlotRendererF(pm);
+        MultiRowXYPlotRendererF(pm);
+        MultiDensityRendererF(pm);
+        MultiLineRendererF(pm);
+        MultiRowLineRendererF(pm);
+        MultiWiggleAddTrackWidgetF(pm);
+        CreateMultiWiggleExtensionF(pm);
+        pm.addToExtensionPoint('Core-guessAdapterForLocation', (cb) => {
+            return (file, index, hint) => {
+                const regexGuess = /\.(bw|bigwig)$/i;
+                const adapterName = 'BigWigAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    bigWigLocation: file,
+                };
+                if (regexGuess.test(fileName) && !hint) {
+                    return obj;
+                }
+                else if (hint === adapterName) {
+                    return obj;
+                }
+                return cb(file, index, hint);
+            };
+        });
+        pm.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'BigWigAdapter') {
+                    return 'QuantitativeTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pm.addRpcMethod(() => new WiggleGetGlobalStats(pm));
+        pm.addRpcMethod(() => new WiggleGetMultiRegionStats(pm));
+        pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
+    }
+}
+export * from './util';
+export { LinearWiggleDisplayReactComponent, Tooltip, WiggleRendering, WiggleBaseRenderer, linearWiggleDisplayModelFactory, };
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/esm/util.d.ts

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+import { FeatureStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare const YSCALEBAR_LABEL_OFFSET = 5;
+export interface ScaleOpts {
+    domain: number[];
+    range: number[];
+    scaleType: string;
+    pivotValue?: number;
+    inverted: boolean;
+}
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+}
+/**
+ * produces a d3-scale from arguments. applies a "nice domain" adjustment
+ *
+ * @param object - containing attributes
+ *   - domain [min,max]
+ *   - range [min,max]
+ *   - bounds [min,max]
+ *   - scaleType (linear or log)
+ *   - pivotValue (number)
+ *   - inverted (boolean)
+ */
+export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+/**
+ * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
+ *
+ * @param scaleType -
+ */
+export declare function getOrigin(scaleType: string): 1 | 0;
+/**
+ * produces a "nice" domain that actually rounds down to 0 for the min
+ * or 0 to the max depending on if all values are positive or negative
+ *
+ * @param object - containing attributes
+ *   - domain [min,max]
+ *   - bounds [min,max]
+ *   - mean
+ *   - stddev
+ *   - scaleType (linear or log)
+ */
+export declare function getNiceDomain({ scaleType, domain, bounds, }: {
+    scaleType: string;
+    domain: number[];
+    bounds: number[];
+}): [number, number];
+export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
+    [key: string]: T[];
+};
+export declare function getStats(self: {
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}, opts: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<FeatureStats>;
+export declare function statsAutorun(self: {
+    estimatedStatsReady: boolean;
+    regionTooLarge: boolean;
+    setLoading: (aborter: AbortController) => void;
+    setError: (error: unknown) => void;
+    updateStats: (stats: FeatureStats, statsRegion: string) => void;
+    renderProps: () => Record<string, unknown>;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}): void;
+export declare function toP(s?: number): number;
+export declare function round(value: number): number;

package/esm/util.js

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+import { scaleLinear, scaleLog, scaleQuantize } from 'd3-scale';
+import { autorun } from 'mobx';
+import { isAbortException, getSession, getContainingView, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { getConf } from '@jbrowse/core/configuration';
+export const YSCALEBAR_LABEL_OFFSET = 5;
+/**
+ * produces a d3-scale from arguments. applies a "nice domain" adjustment
+ *
+ * @param object - containing attributes
+ *   - domain [min,max]
+ *   - range [min,max]
+ *   - bounds [min,max]
+ *   - scaleType (linear or log)
+ *   - pivotValue (number)
+ *   - inverted (boolean)
+ */
+export function getScale({ domain = [], range = [], scaleType, pivotValue, inverted, }) {
+    let scale;
+    const [min, max] = domain;
+    if (min === undefined || max === undefined) {
+        throw new Error('invalid domain');
+    }
+    if (scaleType === 'linear') {
+        scale = scaleLinear();
+    }
+    else if (scaleType === 'log') {
+        scale = scaleLog();
+        scale.base(2);
+    }
+    else if (scaleType === 'quantize') {
+        scale = scaleQuantize();
+    }
+    else {
+        throw new Error('undefined scaleType');
+    }
+    scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
+    scale.nice();
+    const [rangeMin, rangeMax] = range;
+    if (rangeMin === undefined || rangeMax === undefined) {
+        throw new Error('invalid range');
+    }
+    scale.range(inverted ? range.slice().reverse() : range);
+    return scale;
+}
+/**
+ * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
+ *
+ * @param scaleType -
+ */
+export function getOrigin(scaleType /* , pivot, stats */) {
+    // if (pivot) {
+    //   if (pivot === 'mean') {
+    //     return stats.scoreMean || 0
+    //   }
+    //   if (pivot === 'zero') {
+    //     return 0
+    //   }
+    //   return parseFloat()
+    // }
+    // if (scaleType === 'z_score') {
+    //   return stats.scoreMean || 0
+    // }
+    if (scaleType === 'log') {
+        return 1;
+    }
+    return 0;
+}
+/**
+ * produces a "nice" domain that actually rounds down to 0 for the min
+ * or 0 to the max depending on if all values are positive or negative
+ *
+ * @param object - containing attributes
+ *   - domain [min,max]
+ *   - bounds [min,max]
+ *   - mean
+ *   - stddev
+ *   - scaleType (linear or log)
+ */
+export function getNiceDomain({ scaleType, domain, bounds, }) {
+    const [minScore, maxScore] = bounds;
+    let [min, max] = domain;
+    if (scaleType === 'linear') {
+        if (max < 0) {
+            max = 0;
+        }
+        if (min > 0) {
+            min = 0;
+        }
+    }
+    if (scaleType === 'log') {
+        // if the min is 0, assume that it's just something
+        // with no read coverage and that we should ignore it in calculations
+        // if it's greater than 1 pin to 1 for the full range also
+        // otherwise, we may see bigwigs with fractional values
+        if (min === 0 || min > 1) {
+            min = 1;
+        }
+    }
+    if (min === undefined || max === undefined) {
+        throw new Error('invalid domain supplied to stats function');
+    }
+    if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
+        min = minScore;
+    }
+    if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
+        max = maxScore;
+    }
+    const getScaleType = (type) => {
+        if (type === 'linear') {
+            return scaleLinear();
+        }
+        if (type === 'log') {
+            const scale = scaleLog();
+            scale.base(2);
+            return scale;
+        }
+        if (type === 'quantize') {
+            return scaleQuantize();
+        }
+        throw new Error(`undefined scaleType ${type}`);
+    };
+    const scale = getScaleType(scaleType);
+    scale.domain([min, max]);
+    scale.nice();
+    return scale.domain();
+}
+export function groupBy(array, predicate) {
+    return array.reduce((acc, value) => {
+        var _a;
+        const entry = (acc[_a = predicate(value)] || (acc[_a] = []));
+        entry.push(value);
+        return acc;
+    }, {});
+}
+export async function getStats(self, opts) {
+    const { rpcManager } = getSession(self);
+    const nd = getConf(self, 'numStdDev') || 3;
+    const { adapterConfig, autoscaleType } = self;
+    const sessionId = getRpcSessionId(self);
+    const params = {
+        sessionId,
+        adapterConfig,
+        statusCallback: (message) => {
+            if (isAlive(self)) {
+                self.setMessage(message);
+            }
+        },
+        ...opts,
+    };
+    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
+        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalStats', params));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // 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 autoscaleType === 'globalsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
+                scoreMax: scoreMean + nd * scoreStdDev,
+            }
+            : results;
+    }
+    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
+        const { dynamicBlocks, bpPerPx } = getContainingView(self);
+        const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionStats', {
+            ...params,
+            regions: dynamicBlocks.contentBlocks.map(region => {
+                const { start, end } = region;
+                return {
+                    ...JSON.parse(JSON.stringify(region)),
+                    start: Math.floor(start),
+                    end: Math.ceil(end),
+                };
+            }),
+            bpPerPx,
+        }));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // 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 autoscaleType === 'localsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
+                scoreMax: scoreMean + nd * scoreStdDev,
+            }
+            : results;
+    }
+    if (autoscaleType === 'zscale') {
+        return rpcManager.call(sessionId, 'WiggleGetGlobalStats', params);
+    }
+    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
+}
+export function statsAutorun(self) {
+    addDisposer(self, autorun(async () => {
+        try {
+            const aborter = new AbortController();
+            const view = getContainingView(self);
+            self.setLoading(aborter);
+            if (!view.initialized ||
+                !self.estimatedStatsReady ||
+                self.regionTooLarge) {
+                return;
+            }
+            const statsRegion = JSON.stringify(view.dynamicBlocks);
+            const wiggleStats = await getStats(self, {
+                signal: aborter.signal,
+                ...self.renderProps(),
+            });
+            if (isAlive(self)) {
+                self.updateStats(wiggleStats, statsRegion);
+            }
+        }
+        catch (e) {
+            if (!isAbortException(e) && isAlive(self)) {
+                console.error(e);
+                self.setError(e);
+            }
+        }
+    }, { delay: 1000 }));
+}
+export function toP(s = 0) {
+    return +(+s).toPrecision(6);
+}
+export function round(value) {
+    return Math.round(value * 1e5) / 1e5;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "1.7.11",
+  "version": "2.1.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,42 +20,56 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
-    "postbuild": "tsc --build tsconfig.build.json",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/wiggle",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@gmod/bbi": "^1.0.35",
-    "@material-ui/icons": "^4.11.2",
+    "@gmod/bbi": "^2.0.2",
+    "@mui/icons-material": "^5.0.2",
     "@popperjs/core": "^2.11.0",
+    "clone": "^2.1.2",
     "color": "^3.1.1",
-    "d3-scale": "^3.2.3",
-    "react-color": "^2.19.3",
-    "react-d3-axis-mod": "^0.1.3",
+    "d3-color": "^3.0.2",
+    "d3-scale": "^3.0.2",
+    "fast-deep-equal": "^3.1.3",
+    "is-object": "^1.0.1",
+    "react-d3-axis-mod": "^0.1.8",
+    "react-draggable": "^4.4.5",
     "react-popper": "^2.0.0"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx": "^5.0.0",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-data-management": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "@mui/x-data-grid": "^5.0.1",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0"
+    "rxjs": "^6.0.0",
+    "tss-react": "^3.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
 }

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -5,23 +5,17 @@ import {
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { updateStatus } from '@jbrowse/core/util'
+import { updateStatus, Feature } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { map, mergeAll } from 'rxjs/operators'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import { rectifyStats, UnrectifiedFeatureStats } from '@jbrowse/core/util/stats'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 interface WiggleOptions extends BaseOptions {
   resolution?: number
 }
 
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-  private bigwig: BigWig
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  private setupP?: Promise<{ bigwig: BigWig; header: any }>
 
   public static capabilities = [
     'hasResolution',
@@ -29,39 +23,50 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     'hasGlobalStats',
   ]
 
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    this.bigwig = new BigWig({
+  private async setupPre(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
+    const bigwig = new BigWig({
       filehandle: openLocation(
-        readConfObject(config, 'bigWigLocation'),
+        this.getConf('bigWigLocation'),
         this.pluginManager,
       ),
     })
+    const header = await updateStatus(
+      'Downloading bigwig header',
+      statusCallback,
+      () => bigwig.getHeader(opts),
+    )
+    return { bigwig, header }
   }
 
-  private async setup(opts?: BaseOptions) {
-    const { statusCallback = () => {} } = opts || {}
-    return updateStatus('Downloading bigwig header', statusCallback, () =>
-      this.bigwig.getHeader(opts),
-    )
+  async setup(opts?: BaseOptions) {
+    if (!this.setupP) {
+      this.setupP = this.setupPre(opts).catch(e => {
+        this.setupP = undefined
+        throw e
+      })
+    }
+    return this.setupP
   }
 
   public async getRefNames(opts?: BaseOptions) {
-    const { refsByName } = await this.setup(opts)
+    const {
+      header: { refsByName },
+    } = await this.setup(opts)
     return Object.keys(refsByName)
   }
 
   public async refIdToName(refId: number) {
-    const { refsByNumber } = await this.setup()
+    const {
+      header: { refsByNumber },
+    } = await this.setup()
     return refsByNumber[refId]?.name
   }
 
   public async getGlobalStats(opts?: BaseOptions) {
-    const { totalSummary } = await this.setup(opts)
+    const {
+      header: { totalSummary },
+    } = await this.setup(opts)
     return rectifyStats(totalSummary as UnrectifiedFeatureStats)
   }
 
@@ -75,19 +80,32 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     } = opts
     return ObservableCreate<Feature>(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}-${record.end}`,
-            data: { ...record, refName },
-          })
-        }),
-      ).subscribe(observer)
+
+      for (let i = 0; i < feats.length; i++) {
+        const data = feats[i]
+        if (source) {
+          // @ts-ignore
+          data.source = source
+        }
+        const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`
+        // @ts-ignore
+        data.refName = refName
+        data.uniqueId = uniqueId
+        observer.next({
+          // @ts-ignore
+          get: (str: string) => (data as Record<string, unknown>)[str],
+          id: () => uniqueId,
+          // @ts-ignore
+          toJSON: () => data,
+        })
+      }
+      observer.complete()
     }, signal)
   }