@jbrowse/plugin-wiggle 2.17.0 → 3.0.0

package/esm/getQuantitativeStats.js

@@ -1,8 +1,7 @@
-import { isAlive } from 'mobx-state-tree';
-// jbrowse
-import { getSession, getContainingView } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { getConf } from '@jbrowse/core/configuration';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { isAlive } from 'mobx-state-tree';
 export async function getQuantitativeStats(self, opts) {
     const { rpcManager } = getSession(self);
     const numStdDev = getConf(self, 'numStdDev') || 3;
@@ -22,10 +21,6 @@ export async function getQuantitativeStats(self, opts) {
     if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
         const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', 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,
@@ -53,9 +48,6 @@ export async function getQuantitativeStats(self, opts) {
             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,

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

@@ -1,18 +1,18 @@
 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/model").WiggleDisplayModel;
-        }) => import("react").JSX.Element;
+        }) => import("react/jsx-runtime").JSX.Element;
         XYPlotRendererReactComponent: (props: {
-            regions: import("@jbrowse/core/util/types").Region[];
+            regions: import("@jbrowse/core/util").Region[];
             features: Map<string, import("@jbrowse/core/util").Feature>;
             bpPerPx: number;
             width: number;
@@ -21,7 +21,7 @@ export default class WigglePlugin extends Plugin {
             onMouseLeave?: (event: React.MouseEvent) => void;
             onMouseMove?: (event: React.MouseEvent, arg?: string) => void;
             onFeatureClick?: (event: React.MouseEvent, arg?: string) => void;
-        }) => import("react").JSX.Element;
+        }) => import("react/jsx-runtime").JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
         WiggleBaseRenderer: typeof WiggleBaseRenderer;
         linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
@@ -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 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 GuessAdapterF from './GuessAdapter';
 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);
@@ -53,32 +50,7 @@ export default class WigglePlugin extends Plugin {
         MultiRowLineRendererF(pm);
         MultiWiggleAddTrackWorkflowF(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;
-                }
-                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);
-            };
-        });
+        GuessAdapterF(pm);
         pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm));
         pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
@@ -86,5 +58,5 @@ 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.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 export default function SetMinMaxDialog(props: {
     model: {
         minScore: number;
@@ -8,4 +7,4 @@ export default function SetMinMaxDialog(props: {
         setMaxScore: (arg?: number) => void;
     };
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/shared/SetMinMaxDialog.js

@@ -1,6 +1,7 @@
-import React, { useState } from 'react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 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;
@@ -10,21 +11,13 @@ export default function SetMinMaxDialog(props) {
         ? +max > +min
         : true;
     const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "Enter min/max score: "),
-            !ok ? (React.createElement(Typography, { color: "error" }, "Max is greater than or equal to min")) : null,
-            !logOk ? (React.createElement(Typography, { color: "error" }, "Min score should be greater than 0 for log scale")) : null,
-            React.createElement(TextField, { value: min, onChange: event => {
-                    setMin(event.target.value);
-                }, placeholder: "Enter min score" }),
-            React.createElement(TextField, { value: max, onChange: event => {
-                    setMax(event.target.value);
-                }, placeholder: "Enter max score" })),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
-                    model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
-                    model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-                    handleClose();
-                } }, "Submit"))));
+    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track", children: [_jsxs(DialogContent, { children: [_jsx(Typography, { children: "Enter min/max score: " }), !ok ? (_jsx(Typography, { color: "error", children: "Max is greater than or equal to min" })) : null, !logOk ? (_jsx(Typography, { color: "error", children: "Min score should be greater than 0 for log scale" })) : null, _jsx(TextField, { value: min, onChange: event => {
+                            setMin(event.target.value);
+                        }, placeholder: "Enter min score" }), _jsx(TextField, { value: max, onChange: event => {
+                            setMax(event.target.value);
+                        }, placeholder: "Enter max score" })] }), _jsx(DialogActions, { children: _jsx(Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
+                        model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
+                        model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                        handleClose();
+                    }, children: "Submit" }) })] }));
 }

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,
     });