@jbrowse/plugin-wiggle 3.6.5 → 4.0.0

package/dist/index.js

@@ -1,112 +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;
-    };
-})();
-var __exportStar = (this && this.__exportStar) || function(m, exports) {
-    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
-};
-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.Tooltip = exports.LinearWiggleDisplayReactComponent = exports.WiggleRendering = void 0;
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BigWigAdapter_1 = __importDefault(require("./BigWigAdapter"));
-const CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
-const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
-const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
-const LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
-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 MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
-const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
-const MultiWiggleAddTrackWorkflow_1 = __importDefault(require("./MultiWiggleAddTrackWorkflow"));
-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 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_1.ReactComponent,
-            XYPlotRendererReactComponent: XYPlotRenderer_1.ReactComponent,
-            XYPlotRenderer: XYPlotRenderer_1.XYPlotRenderer,
-            WiggleBaseRenderer: WiggleBaseRenderer_1.default,
-            linearWiggleDisplayModelFactory: LinearWiggleDisplay_1.modelFactory,
-            xyPlotRendererConfigSchema: XYPlotRenderer_1.configSchema,
-            utils,
-        };
-    }
-    install(pm) {
-        (0, MultiWiggleAdapter_1.default)(pm);
-        (0, BigWigAdapter_1.default)(pm);
-        (0, QuantitativeTrack_1.default)(pm);
-        (0, MultiQuantitativeTrack_1.default)(pm);
-        (0, LinearWiggleDisplay_1.default)(pm);
-        (0, MultiLinearWiggleDisplay_1.default)(pm);
-        (0, LinePlotRenderer_1.default)(pm);
-        (0, XYPlotRenderer_1.default)(pm);
-        (0, DensityRenderer_1.default)(pm);
-        (0, MultiXYPlotRenderer_1.default)(pm);
-        (0, MultiRowXYPlotRenderer_1.default)(pm);
-        (0, MultiDensityRenderer_1.default)(pm);
-        (0, MultiLineRenderer_1.default)(pm);
-        (0, MultiRowLineRenderer_1.default)(pm);
-        (0, MultiWiggleAddTrackWorkflow_1.default)(pm);
-        (0, CreateMultiWiggleExtension_1.default)(pm);
-        (0, GuessAdapter_1.default)(pm);
-        pm.addRpcMethod(() => new rpcMethods_1.WiggleGetGlobalQuantitativeStats(pm));
-        pm.addRpcMethod(() => new rpcMethods_1.WiggleGetMultiRegionQuantitativeStats(pm));
-        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetSources(pm));
-        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetScoreMatrix(pm));
-        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleClusterScoreMatrix(pm));
-    }
-}
-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_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.d.ts

@@ -1,10 +0,0 @@
-export default function SetMinMaxDialog(props: {
-    model: {
-        minScore: number;
-        maxScore: number;
-        scaleType: string;
-        setMinScore: (arg?: number) => void;
-        setMaxScore: (arg?: number) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/SetMinMaxDialog.js

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetMinMaxDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-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;
-    const [min, setMin] = (0, react_1.useState)(`${minScore !== Number.MIN_VALUE ? minScore : ''}`);
-    const [max, setMax] = (0, react_1.useState)(`${maxScore !== Number.MAX_VALUE ? maxScore : ''}`);
-    const ok = min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
-        ? +max > +min
-        : true;
-    const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Enter min/max score: " }), !ok ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: "Max is greater than or equal to min" })) : null, !logOk ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: "Min score should be greater than 0 for log scale" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { value: min, onChange: event => {
-                            setMin(event.target.value);
-                        }, placeholder: "Enter min score" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: max, onChange: event => {
-                            setMax(event.target.value);
-                        }, placeholder: "Enter max score" })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.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/dist/shared/SharedWiggleConfigSchema.d.ts

@@ -1,66 +0,0 @@
-export default function sharedWiggleConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minimalTicks: {
-        type: string;
-        defaultValue: boolean;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    numStdDev: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    scaleType: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    inverted: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/shared/SharedWiggleConfigSchema.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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");
-function sharedWiggleConfigFactory() {
-    return (0, configuration_1.ConfigurationSchema)('SharedWiggleDisplay', {
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: mobx_state_tree_1.types.enumeration('Autoscale type', [
-                'global',
-                'local',
-                'globalsd',
-                'localsd',
-                'zscore',
-            ]),
-            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
-        },
-        minimalTicks: {
-            type: 'boolean',
-            defaultValue: false,
-            description: 'use the minimal amount of ticks',
-        },
-        minScore: {
-            type: 'number',
-            defaultValue: Number.MIN_VALUE,
-            description: 'minimum value for the y-scale',
-        },
-        maxScore: {
-            type: 'number',
-            description: 'maximum value for the y-scale',
-            defaultValue: Number.MAX_VALUE,
-        },
-        numStdDev: {
-            type: 'number',
-            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
-            defaultValue: 3,
-        },
-        scaleType: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
-            description: 'The type of scale to use',
-            defaultValue: 'linear',
-        },
-        inverted: {
-            type: 'boolean',
-            description: 'draw upside down',
-            defaultValue: false,
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}