@jbrowse/plugin-wiggle 1.7.10 → 2.0.1

package/esm/LinearWiggleDisplay/models/model.js

@@ -0,0 +1,495 @@
+import React, { lazy } from 'react';
+import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { isAbortException, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
+import { autorun, when } from 'mobx';
+import { addDisposer, isAlive, types, getEnv } from 'mobx-state-tree';
+import { axisPropsFromTickScale } from 'react-d3-axis-mod';
+import { getNiceDomain, getScale } from '../../util';
+import Tooltip from '../components/Tooltip';
+import { YScaleBar } from '../components/WiggleDisplayComponent';
+const SetMinMaxDlg = lazy(() => import('../components/SetMinMaxDialog'));
+const SetColorDlg = lazy(() => import('../components/SetColorDialog'));
+// fudge factor for making all labels on the YScalebar visible
+export const YSCALEBAR_LABEL_OFFSET = 5;
+// using a map because it preserves order
+const rendererTypes = new Map([
+    ['xyplot', 'XYPlotRenderer'],
+    ['density', 'DensityRenderer'],
+    ['line', 'LinePlotRenderer'],
+]);
+const stateModelFactory = (pluginManager, configSchema) => types
+    .compose('LinearWiggleDisplay', BaseLinearDisplay, types.model({
+    type: types.literal('LinearWiggleDisplay'),
+    configuration: ConfigurationReference(configSchema),
+    selectedRendering: types.optional(types.string, ''),
+    resolution: types.optional(types.number, 1),
+    fill: types.maybe(types.boolean),
+    color: types.maybe(types.string),
+    posColor: types.maybe(types.string),
+    negColor: types.maybe(types.string),
+    summaryScoreMode: types.maybe(types.string),
+    rendererTypeNameState: types.maybe(types.string),
+    scale: types.maybe(types.string),
+    autoscale: types.maybe(types.string),
+    displayCrossHatches: types.maybe(types.boolean),
+    constraints: types.optional(types.model({
+        max: types.maybe(types.number),
+        min: types.maybe(types.number),
+    }), {}),
+}))
+    .volatile(() => ({
+    statsReady: false,
+    message: undefined,
+    stats: { scoreMin: 0, scoreMax: 50 },
+    statsFetchInProgress: undefined,
+}))
+    .actions(self => ({
+    updateStats({ scoreMin, scoreMax, }) {
+        if (self.stats.scoreMin !== scoreMin ||
+            self.stats.scoreMax !== scoreMax) {
+            self.stats = { scoreMin, scoreMax };
+        }
+        self.statsReady = true;
+    },
+    setColor(color) {
+        self.color = color;
+    },
+    setPosColor(color) {
+        self.posColor = color;
+    },
+    setNegColor(color) {
+        self.negColor = color;
+    },
+    setLoading(aborter) {
+        const { statsFetchInProgress: statsFetch } = self;
+        if (statsFetch !== undefined && !statsFetch.signal.aborted) {
+            statsFetch.abort();
+        }
+        self.statsFetchInProgress = aborter;
+    },
+    // this overrides the BaseLinearDisplayModel to avoid popping up a
+    // feature detail display, but still sets the feature selection on the
+    // model so listeners can detect a click
+    selectFeature(feature) {
+        const session = getSession(self);
+        if (isSelectionContainer(session)) {
+            session.setSelection(feature);
+        }
+    },
+    setResolution(res) {
+        self.resolution = res;
+    },
+    setFill(fill) {
+        self.fill = fill;
+    },
+    toggleLogScale() {
+        if (self.scale !== 'log') {
+            self.scale = 'log';
+        }
+        else {
+            self.scale = 'linear';
+        }
+    },
+    setScaleType(scale) {
+        self.scale = scale;
+    },
+    setSummaryScoreMode(val) {
+        self.summaryScoreMode = val;
+    },
+    setAutoscale(val) {
+        self.autoscale = val;
+    },
+    setMaxScore(val) {
+        self.constraints.max = val;
+    },
+    setRendererType(val) {
+        self.rendererTypeNameState = val;
+    },
+    setMinScore(val) {
+        self.constraints.min = val;
+    },
+    toggleCrossHatches() {
+        self.displayCrossHatches = !self.displayCrossHatches;
+    },
+    setCrossHatches(cross) {
+        self.displayCrossHatches = cross;
+    },
+}))
+    .views(self => ({
+    get TooltipComponent() {
+        return Tooltip;
+    },
+    get adapterTypeName() {
+        return self.adapterConfig.type;
+    },
+    get rendererTypeName() {
+        const viewName = self.rendererTypeNameState || getConf(self, 'defaultRendering');
+        const rendererType = rendererTypes.get(viewName);
+        if (!rendererType) {
+            throw new Error(`unknown alignments view name ${viewName}`);
+        }
+        return rendererType;
+    },
+    // subclasses can define these, as snpcoverage track does
+    get filters() {
+        return undefined;
+    },
+    get scaleType() {
+        return self.scale || getConf(self, 'scaleType');
+    },
+    get maxScore() {
+        const { max } = self.constraints;
+        return max !== null && max !== void 0 ? max : getConf(self, 'maxScore');
+    },
+    get minScore() {
+        const { min } = self.constraints;
+        return min !== null && min !== void 0 ? min : getConf(self, 'minScore');
+    },
+}))
+    .views(self => ({
+    get rendererConfig() {
+        const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
+        const { color, posColor, negColor, summaryScoreMode, scaleType, displayCrossHatches, fill, } = self;
+        return self.rendererType.configSchema.create({
+            ...configBlob,
+            ...(scaleType ? { scaleType } : {}),
+            ...(fill ? { filled: fill } : {}),
+            ...(displayCrossHatches ? { displayCrossHatches } : {}),
+            ...(summaryScoreMode ? { summaryScoreMode } : {}),
+            ...(color ? { color } : {}),
+            ...(negColor ? { negColor } : {}),
+            ...(posColor ? { posColor } : {}),
+        }, getEnv(self));
+    },
+}))
+    .views(self => {
+    let oldDomain = [0, 0];
+    return {
+        get filled() {
+            const { fill, rendererConfig: conf } = self;
+            return fill !== null && fill !== void 0 ? fill : readConfObject(conf, 'filled');
+        },
+        get summaryScoreModeSetting() {
+            const { summaryScoreMode, rendererConfig: conf } = self;
+            return summaryScoreMode !== null && summaryScoreMode !== void 0 ? summaryScoreMode : readConfObject(conf, 'summaryScoreMode');
+        },
+        get domain() {
+            const { stats, scaleType, minScore, maxScore } = self;
+            const ret = getNiceDomain({
+                domain: [stats.scoreMin, stats.scoreMax],
+                bounds: [minScore, maxScore],
+                scaleType,
+            });
+            // avoid weird scalebar if log value and empty region displayed
+            if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
+                return [0, Number.MIN_VALUE];
+            }
+            // avoid returning a new object if it matches the old value
+            if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
+                oldDomain = ret;
+            }
+            return oldDomain;
+        },
+        get needsScalebar() {
+            return (self.rendererTypeName === 'XYPlotRenderer' ||
+                self.rendererTypeName === 'LinePlotRenderer');
+        },
+        get scaleOpts() {
+            return {
+                domain: this.domain,
+                stats: self.stats,
+                autoscaleType: this.autoscaleType,
+                scaleType: self.scaleType,
+                inverted: getConf(self, 'inverted'),
+            };
+        },
+        get canHaveFill() {
+            return self.rendererTypeName === 'XYPlotRenderer';
+        },
+        get autoscaleType() {
+            var _a;
+            return (_a = self.autoscale) !== null && _a !== void 0 ? _a : getConf(self, 'autoscale');
+        },
+        get displayCrossHatchesSetting() {
+            const { displayCrossHatches: hatches, rendererConfig: conf } = self;
+            return hatches !== null && hatches !== void 0 ? hatches : readConfObject(conf, 'displayCrossHatches');
+        },
+    };
+})
+    .views(self => ({
+    get ticks() {
+        const { scaleType, domain, height } = self;
+        const minimalTicks = getConf(self, 'minimalTicks');
+        const range = [height - YSCALEBAR_LABEL_OFFSET, YSCALEBAR_LABEL_OFFSET];
+        const scale = getScale({
+            scaleType,
+            domain,
+            range,
+            inverted: getConf(self, 'inverted'),
+        });
+        const ticks = axisPropsFromTickScale(scale, 4);
+        return height < 100 || minimalTicks
+            ? { ...ticks, values: domain }
+            : ticks;
+    },
+}))
+    .views(self => {
+    const { renderProps: superRenderProps } = self;
+    return {
+        renderProps() {
+            const superProps = superRenderProps();
+            const { filters, ticks, height, resolution, scaleOpts } = self;
+            return {
+                ...superProps,
+                notReady: superProps.notReady || !self.statsReady,
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                config: self.rendererConfig,
+                displayCrossHatches: self.displayCrossHatchesSetting,
+                scaleOpts,
+                resolution,
+                height,
+                ticks,
+                filters,
+            };
+        },
+        get adapterCapabilities() {
+            return pluginManager.getAdapterType(self.adapterTypeName)
+                .adapterCapabilities;
+        },
+        get hasResolution() {
+            return this.adapterCapabilities.includes('hasResolution');
+        },
+        get hasGlobalStats() {
+            return this.adapterCapabilities.includes('hasGlobalStats');
+        },
+    };
+})
+    .views(self => {
+    const { trackMenuItems: superTrackMenuItems } = self;
+    const hasRenderings = getConf(self, 'defaultRendering');
+    return {
+        trackMenuItems() {
+            return [
+                ...superTrackMenuItems(),
+                ...(self.hasResolution
+                    ? [
+                        {
+                            label: 'Resolution',
+                            subMenu: [
+                                {
+                                    label: 'Finer resolution',
+                                    onClick: () => self.setResolution(self.resolution * 5),
+                                },
+                                {
+                                    label: 'Coarser resolution',
+                                    onClick: () => self.setResolution(self.resolution / 5),
+                                },
+                            ],
+                        },
+                        {
+                            label: 'Summary score mode',
+                            subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
+                                label: elt,
+                                onClick: () => self.setSummaryScoreMode(elt),
+                            })),
+                        },
+                    ]
+                    : []),
+                ...(self.canHaveFill
+                    ? [
+                        {
+                            label: self.filled
+                                ? 'Turn off histogram fill'
+                                : 'Turn on histogram fill',
+                            onClick: () => self.setFill(!self.filled),
+                        },
+                    ]
+                    : []),
+                {
+                    label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
+                    onClick: () => self.toggleLogScale(),
+                },
+                {
+                    type: 'checkbox',
+                    label: 'Draw cross hatches',
+                    checked: self.displayCrossHatchesSetting,
+                    onClick: () => self.toggleCrossHatches(),
+                },
+                ...(hasRenderings
+                    ? [
+                        {
+                            label: 'Renderer type',
+                            subMenu: ['xyplot', 'density', 'line'].map(key => ({
+                                label: key,
+                                onClick: () => self.setRendererType(key),
+                            })),
+                        },
+                    ]
+                    : []),
+                {
+                    label: 'Autoscale type',
+                    subMenu: [
+                        ['local', 'Local'],
+                        ...(self.hasGlobalStats
+                            ? [
+                                ['global', 'Global'],
+                                ['globalsd', 'Global ± 3σ'],
+                            ]
+                            : []),
+                        ['localsd', 'Local ± 3σ'],
+                    ].map(([val, label]) => ({
+                        label,
+                        onClick: () => self.setAutoscale(val),
+                    })),
+                },
+                {
+                    label: 'Set min/max score',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            SetMinMaxDlg,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Set color',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            SetColorDlg,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+            ];
+        },
+    };
+})
+    .actions(self => {
+    const { reload: superReload, renderSvg: superRenderSvg } = self;
+    async function getStats(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}'`);
+    }
+    return {
+        // re-runs stats and refresh whole display on reload
+        async reload() {
+            self.setError();
+            const aborter = new AbortController();
+            self.setLoading(aborter);
+            try {
+                const stats = await getStats({
+                    signal: aborter.signal,
+                    ...self.renderProps(),
+                });
+                if (isAlive(self)) {
+                    self.updateStats(stats);
+                    superReload();
+                }
+            }
+            catch (e) {
+                self.setError(e);
+            }
+        },
+        afterAttach() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    const view = getContainingView(self);
+                    if (!view.initialized) {
+                        return;
+                    }
+                    if (!self.estimatedStatsReady) {
+                        return;
+                    }
+                    if (self.regionTooLarge) {
+                        return;
+                    }
+                    const aborter = new AbortController();
+                    self.setLoading(aborter);
+                    const wiggleStats = await getStats({
+                        signal: aborter.signal,
+                        ...self.renderProps(),
+                    });
+                    if (isAlive(self)) {
+                        self.updateStats(wiggleStats);
+                    }
+                }
+                catch (e) {
+                    if (!isAbortException(e) && isAlive(self)) {
+                        console.error(e);
+                        self.setError(e);
+                    }
+                }
+            }, { delay: 1000 }));
+        },
+        async renderSvg(opts) {
+            await when(() => self.statsReady && !!self.regionCannotBeRenderedText);
+            const { needsScalebar, stats } = self;
+            const { offsetPx } = getContainingView(self);
+            return (React.createElement(React.Fragment, null,
+                React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
+                needsScalebar && stats ? (React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+                    React.createElement(YScaleBar, { model: self, orientation: "left" }))) : null));
+        },
+    };
+});
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LinearWiggleDisplay/models/model.js.map

@@ -0,0 +1 @@
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package/esm/WiggleBaseRenderer.d.ts

@@ -0,0 +1,55 @@
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import FeatureRendererType, { RenderArgs as FeatureRenderArgs, RenderArgsSerialized, RenderArgsDeserialized as FeatureRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { ThemeOptions } from '@mui/material';
+import { ScaleOpts } from './util';
+export interface RenderArgs extends FeatureRenderArgs {
+    scaleOpts: ScaleOpts;
+}
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    scaleOpts: ScaleOpts;
+    displayCrossHatches: boolean;
+    ticks: {
+        values: number[];
+    };
+    themeOptions: ThemeOptions;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+}
+export type { RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+export default abstract class WiggleBaseRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        containsNoTransferables: boolean;
+        height: number;
+        width: number;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<string, Feature>;
+        containsNoTransferables: boolean;
+        height: number;
+        width: number;
+        reactElement: JSX.Element;
+        canvasRecordedData?: undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<string, Feature>;
+        containsNoTransferables: boolean;
+        height: number;
+        width: number;
+        imageData: any;
+        canvasRecordedData?: undefined;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        html?: string | undefined;
+    }>;
+    abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<void>;
+}

package/esm/WiggleBaseRenderer.js

@@ -0,0 +1,34 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils';
+export default class WiggleBaseRenderer extends FeatureRendererType {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, regions, bpPerPx } = renderProps;
+        const [region] = regions;
+        const width = (region.end - region.start) / bpPerPx;
+        const res = await renderToAbstractCanvas(width, height, renderProps, (ctx) => this.draw(ctx, {
+            ...renderProps,
+            features,
+        }));
+        const results = await super.render({
+            ...renderProps,
+            ...res,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...res,
+            features,
+            containsNoTransferables: true,
+            height,
+            width,
+        };
+    }
+}
+//# sourceMappingURL=WiggleBaseRenderer.js.map

package/esm/WiggleBaseRenderer.js.map

@@ -0,0 +1 @@
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package/esm/WiggleRPC/rpcMethods.d.ts

@@ -0,0 +1,31 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util/types';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import { FeatureStats } from '@jbrowse/core/util/stats';
+export declare class WiggleGetGlobalStats extends RpcMethodType {
+    name: string;
+    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        sessionId: string;
+    }, rpcDriverClassName: string): Promise<FeatureStats>;
+}
+export declare class WiggleGetMultiRegionStats extends RpcMethodType {
+    name: string;
+    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<FeatureStats>;
+}