@jbrowse/plugin-wiggle 2.17.0 → 2.18.0

package/esm/getQuantitativeStatsAutorun.d.ts

@@ -1,12 +1,12 @@
-import { QuantitativeStats } from '@jbrowse/core/util/stats';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+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: (aborter: AbortController) => void;
+    setStatsLoading: (token: string) => void;
     setError: (error: unknown) => void;
     setMessage: (str: string) => void;
     updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;

package/esm/getQuantitativeStatsAutorun.js

@@ -1,32 +1,30 @@
+import { getContainingView, isAbortException } from '@jbrowse/core/util';
+import { createStopToken } from '@jbrowse/core/util/stopToken';
 import { autorun } from 'mobx';
 import { addDisposer, isAlive } from 'mobx-state-tree';
-// jbrowse
-import { isAbortException, getContainingView } from '@jbrowse/core/util';
-// locals
 import { getQuantitativeStats } from './getQuantitativeStats';
 export function getQuantitativeStatsAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
-            const view = getContainingView(self);
-            const aborter = new AbortController();
-            self.setStatsLoading(aborter);
-            if (!self.quantitativeStatsReady) {
-                return;
-            }
-            const statsRegion = JSON.stringify(view.dynamicBlocks);
-            const wiggleStats = await getQuantitativeStats(self, {
-                signal: aborter.signal,
-                filters: [],
-                currStatsBpPerPx: view.bpPerPx,
-                ...self.adapterProps(),
-            });
-            if (isAlive(self)) {
-                self.updateQuantitativeStats(wiggleStats, statsRegion);
+            if (self.quantitativeStatsReady) {
+                const view = getContainingView(self);
+                const stopToken = createStopToken();
+                self.setStatsLoading(stopToken);
+                const statsRegion = JSON.stringify(view.dynamicBlocks);
+                const wiggleStats = await getQuantitativeStats(self, {
+                    stopToken,
+                    filters: [],
+                    currStatsBpPerPx: view.bpPerPx,
+                    ...self.adapterProps(),
+                });
+                if (isAlive(self)) {
+                    self.updateQuantitativeStats(wiggleStats, statsRegion);
+                }
             }
         }
         catch (e) {
-            console.error(e);
-            if (!isAbortException(e) && isAlive(self)) {
+            if (isAlive(self) && !isAbortException(e)) {
+                console.error(e);
                 self.setError(e);
             }
         }

package/esm/index.d.ts

@@ -1,9 +1,9 @@
 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;
@@ -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 { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
 export type { TooltipContentsComponent } from './Tooltip';
 export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';

package/esm/index.js

@@ -1,27 +1,24 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { getFileName, } from '@jbrowse/core/util/tracks';
-// locals
-import WiggleBaseRenderer from './WiggleBaseRenderer';
+import { getFileName } from '@jbrowse/core/util/tracks';
 import BigWigAdapterF from './BigWigAdapter';
-import QuantitativeTrackF from './QuantitativeTrack';
-import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
-import MultiWiggleAdapterF from './MultiWiggleAdapter';
+import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
 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 LinearWiggleDisplayF, { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
 import MultiDensityRendererF from './MultiDensityRenderer';
 import MultiLineRendererF from './MultiLineRenderer';
+import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay';
+import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
 import MultiRowLineRendererF from './MultiRowLineRenderer';
-import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
+import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer';
+import MultiWiggleAdapterF from './MultiWiggleAdapter';
 import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
+import MultiXYPlotRendererF from './MultiXYPlotRenderer';
+import QuantitativeTrackF from './QuantitativeTrack';
+import WiggleBaseRenderer from './WiggleBaseRenderer';
+import { MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
+import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from './XYPlotRenderer';
 import * as utils from './util';
-import { WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, MultiWiggleGetSources, } from './WiggleRPC/rpcMethods';
-import { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-import { ReactComponent as XYPlotRendererReactComponent, configSchema as xyPlotRendererConfigSchema, XYPlotRenderer, } from './XYPlotRenderer';
 export default class WigglePlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -86,5 +83,5 @@ 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 { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
 export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';

package/esm/shared/SetMinMaxDialog.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 export default function SetMinMaxDialog(props) {
     const { model, handleClose } = props;
     const { minScore, maxScore, scaleType } = model;

package/esm/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/esm/shared/SharedWiggleConfigSchema.js

@@ -1,16 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 export default function sharedWiggleConfigFactory() {
     return ConfigurationSchema('SharedWiggleDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
@@ -23,59 +15,38 @@ export default 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: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            model: 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: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });