@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/src/index.ts

@@ -1,105 +1,77 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+// locals
 import WiggleBaseRenderer from './WiggleBaseRenderer'
 import WiggleRendering from './WiggleRendering'
-import { configSchema as bigWigAdapterConfigSchema } from './BigWigAdapter'
-import DensityRenderer, {
-  configSchema as densityRendererConfigSchema,
-  ReactComponent as DensityRendererReactComponent,
-} from './DensityRenderer'
+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 {
-  configSchemaFactory as linearWiggleDisplayConfigSchemaFactory,
-  modelFactory as linearWiggleDisplayModelFactory,
-  ReactComponent as LinearWiggleDisplayReactComponent,
-  YSCALEBAR_LABEL_OFFSET,
-} from './LinearWiggleDisplay'
-import XYPlotRenderer, {
-  configSchema as xyPlotRendererConfigSchema,
-  ReactComponent as XYPlotRendererReactComponent,
-} from './XYPlotRenderer'
-import LinePlotRenderer, {
-  configSchema as linePlotRendererConfigSchema,
-  ReactComponent as LinePlotRendererReactComponent,
-} from './LinePlotRenderer'
+
 import {
   WiggleGetGlobalStats,
   WiggleGetMultiRegionStats,
+  MultiWiggleGetSources,
 } from './WiggleRPC/rpcMethods'
+
 import {
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
+  ReactComponent as LinearWiggleDisplayReactComponent,
+  modelFactory as linearWiggleDisplayModelFactory,
+  Tooltip,
+} from './LinearWiggleDisplay'
+import { TooltipContentsComponent } from './Tooltip'
+import {
+  ReactComponent as XYPlotRendererReactComponent,
+  configSchema as xyPlotRendererConfigSchema,
+  XYPlotRenderer,
+} from './XYPlotRenderer'
 
 export default class WigglePlugin extends Plugin {
   name = 'WigglePlugin'
 
-  install(pluginManager: PluginManager) {
-    pluginManager.addTrackType(() => {
-      const configSchema = ConfigurationSchema(
-        'QuantitativeTrack',
-        {},
-        { baseConfiguration: createBaseTrackConfig(pluginManager) },
-      )
-      return new TrackType({
-        name: 'QuantitativeTrack',
-        configSchema,
-        stateModel: createBaseTrackModel(
-          pluginManager,
-          'QuantitativeTrack',
-          configSchema,
-        ),
-      })
-    })
-
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearWiggleDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearWiggleDisplay',
-        configSchema,
-        stateModel: linearWiggleDisplayModelFactory(
-          pluginManager,
-          configSchema,
-        ),
-        trackType: 'QuantitativeTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: LinearWiggleDisplayReactComponent,
-      })
-    })
+  install(pm: PluginManager) {
+    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)
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BigWigAdapter',
-          configSchema: bigWigAdapterConfigSchema,
-          adapterCapabilities: [
-            'hasResolution',
-            'hasLocalStats',
-            'hasGlobalStats',
-          ],
-          getAdapterClass: () =>
-            import('./BigWigAdapter/BigWigAdapter').then(r => r.default),
-        }),
-    )
-    pluginManager.addToExtensionPoint(
+    pm.addToExtensionPoint(
       'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
+      (cb: AdapterGuesser) => {
+        return (file: FileLocation, index?: FileLocation, hint?: string) => {
           const regexGuess = /\.(bw|bigwig)$/i
           const adapterName = 'BigWigAdapter'
           const fileName = getFileName(file)
@@ -108,17 +80,17 @@ export default class WigglePlugin extends Plugin {
             bigWigLocation: file,
           }
 
-          if (regexGuess.test(fileName) && !adapterHint) {
+          if (regexGuess.test(fileName) && !hint) {
             return obj
-          } else if (adapterHint === adapterName) {
+          } else if (hint === adapterName) {
             return obj
           }
 
-          return adapterGuesser(file, index, adapterHint)
+          return cb(file, index, hint)
         }
       },
     )
-    pluginManager.addToExtensionPoint(
+    pm.addToExtensionPoint(
       'Core-guessTrackTypeForLocation',
       (trackTypeGuesser: TrackTypeGuesser) => {
         return (adapterName: string) => {
@@ -130,57 +102,31 @@ export default class WigglePlugin extends Plugin {
       },
     )
 
-    pluginManager.addRendererType(
-      () =>
-        new DensityRenderer({
-          name: 'DensityRenderer',
-          ReactComponent: DensityRendererReactComponent,
-          configSchema: densityRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
-    pluginManager.addRendererType(
-      () =>
-        new LinePlotRenderer({
-          name: 'LinePlotRenderer',
-          ReactComponent: LinePlotRendererReactComponent,
-          configSchema: linePlotRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
-    pluginManager.addRendererType(
-      () =>
-        new XYPlotRenderer({
-          name: 'XYPlotRenderer',
-          ReactComponent: XYPlotRendererReactComponent,
-          configSchema: xyPlotRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
-    pluginManager.addRpcMethod(() => new WiggleGetGlobalStats(pluginManager))
-    pluginManager.addRpcMethod(
-      () => new WiggleGetMultiRegionStats(pluginManager),
-    )
+    pm.addRpcMethod(() => new WiggleGetGlobalStats(pm))
+    pm.addRpcMethod(() => new WiggleGetMultiRegionStats(pm))
+    pm.addRpcMethod(() => new MultiWiggleGetSources(pm))
   }
 
   exports = {
     LinearWiggleDisplayReactComponent,
     XYPlotRendererReactComponent,
     XYPlotRenderer,
+    WiggleBaseRenderer,
+
     xyPlotRendererConfigSchema,
     utils,
-    WiggleBaseRenderer,
     linearWiggleDisplayModelFactory,
   }
 }
 
 export * from './util'
 
-export { WiggleRendering }
-export { WiggleBaseRenderer }
-export { LinearWiggleDisplayReactComponent, linearWiggleDisplayModelFactory }
-export { Tooltip } from './LinearWiggleDisplay/components/Tooltip'
-export { YSCALEBAR_LABEL_OFFSET }
+export {
+  LinearWiggleDisplayReactComponent,
+  Tooltip,
+  WiggleRendering,
+  WiggleBaseRenderer,
+  linearWiggleDisplayModelFactory,
+}
+
+export type { TooltipContentsComponent }

package/src/util.ts

@@ -1,4 +1,20 @@
 import { scaleLinear, scaleLog, scaleQuantize } from 'd3-scale'
+import { autorun } from 'mobx'
+import {
+  isAbortException,
+  getSession,
+  getContainingView,
+} from '@jbrowse/core/util'
+import { FeatureStats } from '@jbrowse/core/util/stats'
+import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import { addDisposer, isAlive } from 'mobx-state-tree'
+
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { AnyConfigurationModel, getConf } from '@jbrowse/core/configuration'
+
+type LGV = LinearGenomeViewModel
+
+export const YSCALEBAR_LABEL_OFFSET = 5
 
 export interface ScaleOpts {
   domain: number[]
@@ -7,6 +23,13 @@ export interface ScaleOpts {
   pivotValue?: number
   inverted: boolean
 }
+
+export interface Source {
+  name: string
+  color?: string
+  group?: string
+}
+
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -143,3 +166,154 @@ export function getNiceDomain({
   scale.nice()
   return scale.domain() as [number, number]
 }
+
+export function groupBy<T>(array: T[], predicate: (v: T) => string) {
+  return array.reduce((acc, value) => {
+    const entry = (acc[predicate(value)] ||= [])
+    entry.push(value)
+    return acc
+  }, {} as { [key: string]: T[] })
+}
+
+export async function getStats(
+  self: {
+    adapterConfig: AnyConfigurationModel
+    autoscaleType: string
+    setMessage: (str: string) => void
+  },
+  opts: {
+    headers?: Record<string, string>
+    signal?: AbortSignal
+    filters?: string[]
+  },
+): Promise<FeatureStats> {
+  const { rpcManager } = getSession(self)
+  const nd = getConf(self, 'numStdDev') || 3
+  const { adapterConfig, autoscaleType } = self
+  const sessionId = getRpcSessionId(self)
+  const params = {
+    sessionId,
+    adapterConfig,
+    statusCallback: (message: string) => {
+      if (isAlive(self)) {
+        self.setMessage(message)
+      }
+    },
+    ...opts,
+  }
+
+  if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
+    const results: FeatureStats = (await rpcManager.call(
+      sessionId,
+      'WiggleGetGlobalStats',
+      params,
+    )) as FeatureStats
+    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) as LGV
+    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,
+      },
+    )) as FeatureStats
+    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,
+    ) as Promise<FeatureStats>
+  }
+  throw new Error(`invalid autoscaleType '${autoscaleType}'`)
+}
+
+export 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
+}) {
+  addDisposer(
+    self,
+    autorun(
+      async () => {
+        try {
+          const aborter = new AbortController()
+          const view = getContainingView(self) as LGV
+          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: number) {
+  return Math.round(value * 1e5) / 1e5
+}

package/dist/BigWigAdapter/BigWigAdapter.test.js

@@ -1,157 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _BigWigAdapter = _interopRequireDefault(require("./BigWigAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-describe('adapter can fetch features from volvox.bw', function () {
-  var adapter;
-  beforeEach(function () {
-    adapter = new _BigWigAdapter.default(_configSchema.default.create({
-      bigWigLocation: {
-        localPath: require.resolve('./test_data/volvox.bw'),
-        locationType: 'LocalPathLocation'
-      }
-    }));
-  });
-  it('test basic aspects of getfeatures', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var features, featuresArray, featuresJsonArray;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            features = adapter.getFeatures({
-              refName: 'ctgA',
-              start: 0,
-              end: 20000,
-              assemblyName: 'volvox'
-            });
-            _context.t0 = expect;
-            _context.next = 4;
-            return adapter.refIdToName(0);
-
-          case 4:
-            _context.t1 = _context.sent;
-            (0, _context.t0)(_context.t1).toBe('ctgA');
-            _context.t2 = expect;
-            _context.next = 9;
-            return adapter.refIdToName(1);
-
-          case 9:
-            _context.t3 = _context.sent;
-            (0, _context.t2)(_context.t3).toBe(undefined);
-            _context.t4 = expect;
-            _context.next = 14;
-            return adapter.hasDataForRefName('ctgA');
-
-          case 14:
-            _context.t5 = _context.sent;
-            (0, _context.t4)(_context.t5).toBe(true);
-            _context.t6 = expect;
-            _context.next = 19;
-            return adapter.hasDataForRefName('ctgB');
-
-          case 19:
-            _context.t7 = _context.sent;
-            (0, _context.t6)(_context.t7).toBe(false);
-            _context.next = 23;
-            return features.pipe((0, _operators.toArray)()).toPromise();
-
-          case 23:
-            featuresArray = _context.sent;
-            featuresJsonArray = featuresArray.map(function (f) {
-              return f.toJSON();
-            });
-            expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
-
-          case 26:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  it('adapter can fetch stats from volvox.bw', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            _context2.t0 = expect;
-            _context2.next = 3;
-            return adapter.getGlobalStats();
-
-          case 3:
-            _context2.t1 = _context2.sent;
-            (0, _context2.t0)(_context2.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-  it('get region stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            _context3.t0 = expect;
-            _context3.next = 3;
-            return adapter.getRegionStats({
-              refName: 'ctgA',
-              start: 10000,
-              end: 40000,
-              assemblyName: 'volvox'
-            });
-
-          case 3:
-            _context3.t1 = _context3.sent;
-            (0, _context3.t0)(_context3.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  })));
-  it('get local stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-    return _regenerator.default.wrap(function _callee4$(_context4) {
-      while (1) {
-        switch (_context4.prev = _context4.next) {
-          case 0:
-            _context4.t0 = expect;
-            _context4.next = 3;
-            return adapter.getMultiRegionStats([{
-              refName: 'ctgA',
-              start: 10000,
-              end: 39999,
-              assemblyName: 'volvox'
-            }, {
-              refName: 'ctgB',
-              start: 0,
-              end: 99,
-              assemblyName: 'volvox'
-            }]);
-
-          case 3:
-            _context4.t1 = _context4.sent;
-            (0, _context4.t0)(_context4.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context4.stop();
-        }
-      }
-    }, _callee4);
-  })));
-});

package/dist/DensityRenderer/DensityRenderer.test.js

@@ -1,88 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _offscreenCanvasUtils = require("@jbrowse/core/util/offscreenCanvasUtils");
-
-var _ = _interopRequireWildcard(require("."));
-
-var _canvas = require("canvas");
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-global.nodeImage = _canvas.Image;
-global.nodeCreateCanvas = _canvas.createCanvas;
-var pluginManager = {};
-var renderer = new _.default({
-  name: 'DensityRenderer',
-  ReactComponent: _.ReactComponent,
-  configSchema: _.configSchema,
-  pluginManager: pluginManager
-});
-test('inverted mode and reversed', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var renderProps, res;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          renderProps = {
-            features: [new _simpleFeature.default({
-              id: 't1',
-              data: {
-                start: 1,
-                end: 100,
-                score: 1
-              }
-            }), new _simpleFeature.default({
-              id: 't2',
-              data: {
-                start: 101,
-                end: 200,
-                score: 2
-              }
-            })],
-            regions: [{
-              end: 100,
-              start: 1,
-              reversed: true,
-              refName: 'ctgA',
-              assemblyName: 'volvox'
-            }],
-            scaleOpts: {
-              domain: [0, 100],
-              inverted: true,
-              scaleType: 'linear'
-            },
-            bpPerPx: 3,
-            highResolutionScaling: 1,
-            config: {},
-            height: 100
-          };
-          _context.next = 3;
-          return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(1000, 200, renderProps, function (ctx) {
-            return renderer.draw(ctx, renderProps);
-          });
-
-        case 3:
-          res = _context.sent;
-          expect(res).toMatchSnapshot({
-            imageData: expect.any(Object)
-          });
-
-        case 5:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));