@jbrowse/plugin-wiggle 2.16.1 → 2.18.0

package/dist/getQuantitativeStats.js

@@ -0,0 +1,70 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getQuantitativeStats = getQuantitativeStats;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_state_tree_1 = require("mobx-state-tree");
+async function getQuantitativeStats(self, opts) {
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const numStdDev = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
+    const { adapterConfig, autoscaleType } = self;
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+    const { currStatsBpPerPx } = opts;
+    const params = {
+        sessionId,
+        adapterConfig,
+        statusCallback: (message) => {
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setMessage(message);
+            }
+        },
+        ...opts,
+    };
+    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
+        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        return autoscaleType === 'globalsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
+                currStatsBpPerPx,
+            }
+            : {
+                ...results,
+                currStatsBpPerPx,
+            };
+    }
+    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
+        const { dynamicBlocks, bpPerPx } = (0, util_1.getContainingView)(self);
+        const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
+            ...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;
+        return autoscaleType === 'localsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
+                currStatsBpPerPx,
+            }
+            : {
+                ...results,
+                currStatsBpPerPx,
+            };
+    }
+    if (autoscaleType === 'zscale') {
+        return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
+    }
+    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
+}

package/dist/getQuantitativeStatsAutorun.d.ts

@@ -0,0 +1,13 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { QuantitativeStats } from '@jbrowse/core/util/stats';
+export declare function getQuantitativeStatsAutorun(self: {
+    quantitativeStatsReady: boolean;
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    adapterProps: () => Record<string, unknown>;
+    setStatsLoading: (token: string) => void;
+    setError: (error: unknown) => void;
+    setMessage: (str: string) => void;
+    updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
+}): void;

package/dist/getQuantitativeStatsAutorun.js

@@ -0,0 +1,35 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getQuantitativeStatsAutorun = getQuantitativeStatsAutorun;
+const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const getQuantitativeStats_1 = require("./getQuantitativeStats");
+function getQuantitativeStatsAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            if (self.quantitativeStatsReady) {
+                const view = (0, util_1.getContainingView)(self);
+                const stopToken = (0, stopToken_1.createStopToken)();
+                self.setStatsLoading(stopToken);
+                const statsRegion = JSON.stringify(view.dynamicBlocks);
+                const wiggleStats = await (0, getQuantitativeStats_1.getQuantitativeStats)(self, {
+                    stopToken,
+                    filters: [],
+                    currStatsBpPerPx: view.bpPerPx,
+                    ...self.adapterProps(),
+                });
+                if ((0, mobx_state_tree_1.isAlive)(self)) {
+                    self.updateQuantitativeStats(wiggleStats, statsRegion);
+                }
+            }
+        }
+        catch (e) {
+            if ((0, mobx_state_tree_1.isAlive)(self) && !(0, util_1.isAbortException)(e)) {
+                console.error(e);
+                self.setError(e);
+            }
+        }
+    }, { delay: 1000 }));
+}

package/dist/index.d.ts

@@ -1,15 +1,15 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-import WiggleBaseRenderer from './WiggleBaseRenderer';
-import * as utils from './util';
 import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay';
+import WiggleBaseRenderer from './WiggleBaseRenderer';
 import { XYPlotRenderer } from './XYPlotRenderer';
+import * as utils from './util';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class WigglePlugin extends Plugin {
     name: string;
     install(pm: PluginManager): void;
     exports: {
         LinearWiggleDisplayReactComponent: (props: {
-            model: import("./LinearWiggleDisplay/models/model").WiggleDisplayModel;
+            model: import("./LinearWiggleDisplay/model").WiggleDisplayModel;
         }) => import("react").JSX.Element;
         XYPlotRendererReactComponent: (props: {
             regions: import("@jbrowse/core/util/types").Region[];
@@ -83,6 +83,6 @@ export default class WigglePlugin extends Plugin {
 }
 export * from './util';
 export { default as WiggleRendering } from './WiggleRendering';
-export { Tooltip, ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-export { type TooltipContentsComponent } from './Tooltip';
+export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
+export type { TooltipContentsComponent } from './Tooltip';
 export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';

package/dist/index.js

@@ -29,42 +29,39 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.WiggleBaseRenderer = exports.linearWiggleDisplayModelFactory = exports.LinearWiggleDisplayReactComponent = exports.Tooltip = exports.WiggleRendering = void 0;
+exports.WiggleBaseRenderer = exports.linearWiggleDisplayModelFactory = exports.Tooltip = exports.LinearWiggleDisplayReactComponent = exports.WiggleRendering = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
-// locals
-const WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
 const BigWigAdapter_1 = __importDefault(require("./BigWigAdapter"));
-const QuantitativeTrack_1 = __importDefault(require("./QuantitativeTrack"));
-const MultiQuantitativeTrack_1 = __importDefault(require("./MultiQuantitativeTrack"));
-const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
+const CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
 const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
-const XYPlotRenderer_1 = __importDefault(require("./XYPlotRenderer"));
 const LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
-const LinearWiggleDisplay_1 = __importDefault(require("./LinearWiggleDisplay"));
-const MultiLinearWiggleDisplay_1 = __importDefault(require("./MultiLinearWiggleDisplay"));
-const MultiXYPlotRenderer_1 = __importDefault(require("./MultiXYPlotRenderer"));
-const MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+const LinearWiggleDisplay_1 = __importStar(require("./LinearWiggleDisplay"));
 const MultiDensityRenderer_1 = __importDefault(require("./MultiDensityRenderer"));
 const MultiLineRenderer_1 = __importDefault(require("./MultiLineRenderer"));
+const MultiLinearWiggleDisplay_1 = __importDefault(require("./MultiLinearWiggleDisplay"));
+const MultiQuantitativeTrack_1 = __importDefault(require("./MultiQuantitativeTrack"));
 const MultiRowLineRenderer_1 = __importDefault(require("./MultiRowLineRenderer"));
-const CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
+const MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
 const MultiWiggleAddTrackWorkflow_1 = __importDefault(require("./MultiWiggleAddTrackWorkflow"));
-const utils = __importStar(require("./util"));
+const MultiXYPlotRenderer_1 = __importDefault(require("./MultiXYPlotRenderer"));
+const QuantitativeTrack_1 = __importDefault(require("./QuantitativeTrack"));
+const WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
 const rpcMethods_1 = require("./WiggleRPC/rpcMethods");
-const LinearWiggleDisplay_2 = require("./LinearWiggleDisplay");
-const XYPlotRenderer_2 = require("./XYPlotRenderer");
+const XYPlotRenderer_1 = __importStar(require("./XYPlotRenderer"));
+const utils = __importStar(require("./util"));
 class WigglePlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'WigglePlugin';
         this.exports = {
-            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_2.ReactComponent,
-            XYPlotRendererReactComponent: XYPlotRenderer_2.ReactComponent,
-            XYPlotRenderer: XYPlotRenderer_2.XYPlotRenderer,
+            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_1.ReactComponent,
+            XYPlotRendererReactComponent: XYPlotRenderer_1.ReactComponent,
+            XYPlotRenderer: XYPlotRenderer_1.XYPlotRenderer,
             WiggleBaseRenderer: WiggleBaseRenderer_1.default,
-            linearWiggleDisplayModelFactory: LinearWiggleDisplay_2.modelFactory,
-            xyPlotRendererConfigSchema: XYPlotRenderer_2.configSchema,
+            linearWiggleDisplayModelFactory: LinearWiggleDisplay_1.modelFactory,
+            xyPlotRendererConfigSchema: XYPlotRenderer_1.configSchema,
             utils,
         };
     }
@@ -120,9 +117,9 @@ exports.default = WigglePlugin;
 __exportStar(require("./util"), exports);
 var WiggleRendering_1 = require("./WiggleRendering");
 Object.defineProperty(exports, "WiggleRendering", { enumerable: true, get: function () { return __importDefault(WiggleRendering_1).default; } });
-var LinearWiggleDisplay_3 = require("./LinearWiggleDisplay");
-Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return LinearWiggleDisplay_3.Tooltip; } });
-Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_3.ReactComponent; } });
-Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_3.modelFactory; } });
+var LinearWiggleDisplay_2 = require("./LinearWiggleDisplay");
+Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_2.ReactComponent; } });
+Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return LinearWiggleDisplay_2.Tooltip; } });
+Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_2.modelFactory; } });
 var WiggleBaseRenderer_2 = require("./WiggleBaseRenderer");
 Object.defineProperty(exports, "WiggleBaseRenderer", { enumerable: true, get: function () { return __importDefault(WiggleBaseRenderer_2).default; } });

package/dist/shared/SetMinMaxDialog.js

@@ -25,8 +25,8 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SetMinMaxDialog;
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 function SetMinMaxDialog(props) {
     const { model, handleClose } = props;
     const { minScore, maxScore, scaleType } = model;

package/{esm/shared/configShared.d.ts → dist/shared/SharedWiggleConfigSchema.d.ts}

@@ -1,62 +1,36 @@
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 export default function sharedWiggleConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     autoscale: {
         type: string;
         defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
     };
-    /**
-     * #slot
-     */
     minimalTicks: {
         type: string;
         defaultValue: boolean;
         description: string;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     numStdDev: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     inverted: {
         type: string;
         description: string;

package/dist/shared/{configShared.js → SharedWiggleConfigSchema.js}

@@ -4,16 +4,8 @@ exports.default = sharedWiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 function sharedWiggleConfigFactory() {
     return (0, configuration_1.ConfigurationSchema)('SharedWiggleDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
@@ -26,59 +18,38 @@ function sharedWiggleConfigFactory() {
             ]),
             description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
         },
-        /**
-         * #slot
-         */
         minimalTicks: {
             type: 'boolean',
             defaultValue: false,
             description: 'use the minimal amount of ticks',
         },
-        /**
-         * #slot
-         */
         minScore: {
             type: 'number',
             defaultValue: Number.MIN_VALUE,
             description: 'minimum value for the y-scale',
         },
-        /**
-         * #slot
-         */
         maxScore: {
             type: 'number',
             description: 'maximum value for the y-scale',
             defaultValue: Number.MAX_VALUE,
         },
-        /**
-         * #slot
-         */
         numStdDev: {
             type: 'number',
             description: 'number of standard deviations to use for autoscale types globalsd or localsd',
             defaultValue: 3,
         },
-        /**
-         * #slot
-         */
         scaleType: {
             type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
             description: 'The type of scale to use',
             defaultValue: 'linear',
         },
-        /**
-         * #slot
-         */
         inverted: {
             type: 'boolean',
             description: 'draw upside down',
             defaultValue: false,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });