@jbrowse/plugin-wiggle 3.6.5 → 4.0.0

package/dist/shared/SharedWiggleMixin.js

@@ -1,343 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SharedWiggleMixin;
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_2 = require("../util");
-const SetMinMaxDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SetMinMaxDialog'))));
-function SharedWiggleMixin(configSchema) {
-    return mobx_state_tree_1.types
-        .compose(plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        selectedRendering: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
-        resolution: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
-        fill: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        minSize: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        color: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        posColor: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        negColor: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        summaryScoreMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        rendererTypeNameState: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        scale: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        autoscale: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        displayCrossHatches: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        constraints: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-            max: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-            min: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        }), {}),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-    }))
-        .volatile(() => ({
-        message: undefined,
-        stats: undefined,
-        statsFetchInProgress: undefined,
-    }))
-        .actions(self => ({
-        updateQuantitativeStats(stats) {
-            const { currStatsBpPerPx, scoreMin, scoreMax } = stats;
-            const EPSILON = 0.000001;
-            if (!self.stats ||
-                Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
-                Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
-                self.stats = {
-                    currStatsBpPerPx,
-                    scoreMin,
-                    scoreMax,
-                };
-            }
-        },
-        setColor(color) {
-            self.color = color;
-        },
-        setPosColor(color) {
-            self.posColor = color;
-        },
-        setNegColor(color) {
-            self.negColor = color;
-        },
-        setStatsLoading(arg) {
-            if (self.statsFetchInProgress) {
-                (0, stopToken_1.stopStopToken)(self.statsFetchInProgress);
-            }
-            self.statsFetchInProgress = arg;
-        },
-        selectFeature(feature) {
-            const session = (0, util_1.getSession)(self);
-            if ((0, util_1.isSelectionContainer)(session)) {
-                session.setSelection(feature);
-            }
-        },
-        setResolution(res) {
-            self.resolution = res;
-        },
-        setFill(fill) {
-            if (fill === 0) {
-                self.fill = true;
-                self.minSize = 0;
-            }
-            else if (fill === 1) {
-                self.fill = false;
-                self.minSize = 1;
-            }
-            else if (fill === 2) {
-                self.fill = false;
-                self.minSize = 2;
-            }
-        },
-        toggleLogScale() {
-            self.scale = self.scale === 'log' ? 'linear' : 'log';
-        },
-        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 adapterTypeName() {
-            return self.adapterConfig.type;
-        },
-        get rendererTypeNameSimple() {
-            var _a;
-            return ((_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'defaultRendering'));
-        },
-        get filters() {
-            return undefined;
-        },
-        get scaleType() {
-            var _a;
-            return (_a = self.scale) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'scaleType');
-        },
-        get maxScore() {
-            var _a;
-            return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'maxScore');
-        },
-        get minScore() {
-            var _a;
-            return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'minScore');
-        },
-    }))
-        .views(self => ({
-        get adapterCapabilities() {
-            const type = self.adapterTypeName;
-            const { pluginManager } = (0, util_1.getEnv)(self);
-            return pluginManager.getAdapterType(type).adapterCapabilities;
-        },
-        get rendererConfig() {
-            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
-            return self.rendererType.configSchema.create({
-                ...configBlob,
-                ...(scaleType ? { scaleType } : {}),
-                ...(fill !== undefined ? { filled: fill } : {}),
-                ...(displayCrossHatches !== undefined
-                    ? { displayCrossHatches }
-                    : {}),
-                ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
-                ...(color !== undefined ? { color } : {}),
-                ...(negColor !== undefined ? { negColor } : {}),
-                ...(posColor !== undefined ? { posColor } : {}),
-                ...(minSize !== undefined ? { minSize } : {}),
-            }, (0, util_1.getEnv)(self));
-        },
-        get autoscaleType() {
-            var _a;
-            return (_a = self.autoscale) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'autoscale');
-        },
-    }))
-        .views(self => {
-        let oldDomain = [0, 0];
-        return {
-            get domain() {
-                const { stats, scaleType, minScore, maxScore } = self;
-                if (!stats) {
-                    return undefined;
-                }
-                const ret = (0, util_2.getNiceDomain)({
-                    domain: [stats.scoreMin, stats.scoreMax],
-                    bounds: [minScore, maxScore],
-                    scaleType,
-                });
-                if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
-                    return [0, Number.MIN_VALUE];
-                }
-                if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
-                    oldDomain = ret;
-                }
-                return oldDomain;
-            },
-        };
-    })
-        .views(self => ({
-        get filled() {
-            var _a;
-            return ((_a = self.fill) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'filled'));
-        },
-        get summaryScoreModeSetting() {
-            var _a;
-            return ((_a = self.summaryScoreMode) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'summaryScoreMode'));
-        },
-        get scaleOpts() {
-            return {
-                domain: self.domain,
-                stats: self.stats,
-                autoscaleType: self.autoscaleType,
-                scaleType: self.scaleType,
-                inverted: (0, configuration_1.getConf)(self, 'inverted'),
-            };
-        },
-        get canHaveFill() {
-            return self.rendererTypeName === 'XYPlotRenderer';
-        },
-        get displayCrossHatchesSetting() {
-            var _a;
-            return ((_a = self.displayCrossHatches) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'displayCrossHatches'));
-        },
-        get hasResolution() {
-            return self.adapterCapabilities.includes('hasResolution');
-        },
-        get hasGlobalStats() {
-            return self.adapterCapabilities.includes('hasGlobalStats');
-        },
-    }))
-        .views(self => ({
-        scoreTrackMenuItems() {
-            return [
-                ...(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,
-                                type: 'radio',
-                                checked: self.summaryScoreModeSetting === elt,
-                                onClick: () => {
-                                    self.setSummaryScoreMode(elt);
-                                },
-                            })),
-                        },
-                    ]
-                    : []),
-                {
-                    label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
-                    onClick: () => {
-                        self.toggleLogScale();
-                    },
-                },
-                {
-                    label: 'Autoscale type',
-                    subMenu: [
-                        ['local', 'Local'],
-                        ...(self.hasGlobalStats
-                            ? [
-                                ['global', 'Global'],
-                                ['globalsd', 'Global ± 3σ'],
-                            ]
-                            : []),
-                        ['localsd', 'Local ± 3σ'],
-                    ].map(([val, label]) => ({
-                        label,
-                        type: 'radio',
-                        checked: self.autoscaleType === val,
-                        onClick: () => {
-                            self.setAutoscale(val);
-                        },
-                    })),
-                },
-                {
-                    label: 'Set min/max score',
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            SetMinMaxDialog,
-                            {
-                                model: self,
-                                handleClose,
-                            },
-                        ]);
-                    },
-                },
-            ];
-        },
-    }))
-        .actions(self => {
-        const { reload: superReload } = self;
-        return {
-            async reload() {
-                self.setError();
-                superReload();
-            },
-        };
-    });
-}

package/dist/shared/YScaleBar.d.ts

@@ -1,9 +0,0 @@
-import type { axisPropsFromTickScale } from 'react-d3-axis-mod';
-type Ticks = ReturnType<typeof axisPropsFromTickScale>;
-declare const YScaleBar: ({ model, orientation, }: {
-    model: {
-        ticks?: Ticks;
-    };
-    orientation?: string;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default YScaleBar;

package/dist/shared/YScaleBar.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const react_d3_axis_mod_1 = require("react-d3-axis-mod");
-const YScaleBar = (0, mobx_react_1.observer)(function ({ model, orientation, }) {
-    const { ticks } = model;
-    const theme = (0, material_1.useTheme)();
-    return ticks ? ((0, jsx_runtime_1.jsx)(react_d3_axis_mod_1.Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? react_d3_axis_mod_1.LEFT : react_d3_axis_mod_1.RIGHT }, bg: theme.palette.background.default, fg: theme.palette.text.primary })) : null;
-});
-exports.default = YScaleBar;

package/dist/util.d.ts

@@ -1,24 +0,0 @@
-export declare const YSCALEBAR_LABEL_OFFSET = 5;
-export interface ScaleOpts {
-    domain: number[];
-    range: number[];
-    scaleType: string;
-    pivotValue?: number;
-    inverted?: boolean;
-}
-export interface Source {
-    baseUri?: string;
-    name: string;
-    color?: string;
-    group?: string;
-}
-export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleLogarithmic<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
-export declare function getOrigin(scaleType: string): 1 | 0;
-export declare function getNiceDomain({ scaleType, domain, bounds, }: {
-    scaleType: string;
-    domain: readonly [number, number];
-    bounds: readonly [number | undefined, number | undefined];
-}): [number, number];
-export declare function toP(s?: number): number;
-export declare function round(value: number): number;
-export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;

package/dist/util.js

@@ -1,105 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.YSCALEBAR_LABEL_OFFSET = void 0;
-exports.getScale = getScale;
-exports.getOrigin = getOrigin;
-exports.getNiceDomain = getNiceDomain;
-exports.toP = toP;
-exports.round = round;
-exports.fillRectCtx = fillRectCtx;
-const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
-exports.YSCALEBAR_LABEL_OFFSET = 5;
-function getScale({ domain = [], range = [], scaleType, pivotValue, inverted, }) {
-    let scale;
-    const [min, max] = domain;
-    if (min === undefined || max === undefined) {
-        throw new Error('invalid domain');
-    }
-    if (scaleType === 'linear') {
-        scale = (0, d3_scale_1.scaleLinear)();
-    }
-    else if (scaleType === 'log') {
-        scale = (0, d3_scale_1.scaleLog)().base(2);
-    }
-    else if (scaleType === 'quantize') {
-        scale = (0, d3_scale_1.scaleQuantize)();
-    }
-    else {
-        throw new Error('undefined scaleType');
-    }
-    scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
-    scale.nice();
-    const [rangeMin, rangeMax] = range;
-    if (rangeMin === undefined || rangeMax === undefined) {
-        throw new Error('invalid range');
-    }
-    scale.range(inverted ? range.slice().reverse() : range);
-    return scale;
-}
-function getOrigin(scaleType) {
-    if (scaleType === 'log') {
-        return 1;
-    }
-    return 0;
-}
-function getNiceDomain({ scaleType, domain, bounds, }) {
-    const [minScore, maxScore] = bounds;
-    let [min, max] = domain;
-    if (scaleType === 'linear') {
-        if (max < 0) {
-            max = 0;
-        }
-        if (min > 0) {
-            min = 0;
-        }
-    }
-    if (scaleType === 'log') {
-        if (min >= 0 && max > 1) {
-            min = 1;
-        }
-    }
-    if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
-        min = minScore;
-    }
-    if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
-        max = maxScore;
-    }
-    const getScaleType = (type) => {
-        if (type === 'linear') {
-            return (0, d3_scale_1.scaleLinear)();
-        }
-        if (type === 'log') {
-            const scale = (0, d3_scale_1.scaleLog)();
-            scale.base(2);
-            return scale;
-        }
-        if (type === 'quantize') {
-            return (0, d3_scale_1.scaleQuantize)();
-        }
-        throw new Error(`undefined scaleType ${type}`);
-    };
-    const scale = getScaleType(scaleType);
-    scale.domain([min, max]);
-    scale.nice();
-    return scale.domain();
-}
-function toP(s = 0) {
-    return +(+s).toPrecision(6);
-}
-function round(value) {
-    return Math.round(value * 1e5) / 1e5;
-}
-function fillRectCtx(x, y, width, height, ctx, color) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(x, y, width, height);
-}

package/esm/WiggleBaseRenderer.d.ts

@@ -1,57 +0,0 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { ScaleOpts, Source } from './util';
-import type { RenderArgs as FeatureRenderArgs, RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Feature } from '@jbrowse/core/util';
-import type { ThemeOptions } from '@mui/material';
-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[];
-    };
-    inverted: boolean;
-    themeOptions: ThemeOptions;
-    statusCallback?: (arg: string) => void;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    inverted: boolean;
-}
-export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
-    sources: Source[];
-}
-export default abstract class WiggleBaseRenderer extends FeatureRendererType {
-    supportsSVG: boolean;
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        reactElement: React.ReactElement;
-        html?: string;
-    }>;
-    abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;
-}
-export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/esm/WiggleBaseRenderer.js

@@ -1,36 +0,0 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { renderToAbstractCanvas, updateStatus } from '@jbrowse/core/util';
-export default class WiggleBaseRenderer extends FeatureRendererType {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
-    async render(renderProps) {
-        const features = await this.getFeatures(renderProps);
-        const { inverted, height, regions, bpPerPx, statusCallback = () => { }, } = renderProps;
-        const region = regions[0];
-        const width = (region.end - region.start) / bpPerPx;
-        const { reducedFeatures, ...rest } = await updateStatus('Rendering plot', statusCallback, () => renderToAbstractCanvas(width, height, renderProps, ctx => this.draw(ctx, {
-            ...renderProps,
-            features,
-            inverted,
-        })));
-        const results = await super.render({
-            ...renderProps,
-            ...rest,
-            features,
-            height,
-            width,
-        });
-        return {
-            ...results,
-            ...rest,
-            features: reducedFeatures
-                ? new Map(reducedFeatures.map(r => [r.id(), r]))
-                : results.features,
-            height,
-            width,
-            containsNoTransferables: true,
-        };
-    }
-}

package/esm/WiggleRPC/type.js

@@ -1 +0,0 @@
-"use strict";