@jbrowse/plugin-wiggle 2.17.0 → 3.0.0

package/dist/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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);
 };
@@ -29,42 +39,39 @@ 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.LinearWiggleDisplayReactComponent = exports.Tooltip = exports.WiggleRendering = void 0;
+exports.WiggleBaseRenderer = exports.linearWiggleDisplayModelFactory = exports.Tooltip = exports.LinearWiggleDisplayReactComponent = exports.WiggleRendering = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
-// locals
-const WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
 const BigWigAdapter_1 = __importDefault(require("./BigWigAdapter"));
-const QuantitativeTrack_1 = __importDefault(require("./QuantitativeTrack"));
-const MultiQuantitativeTrack_1 = __importDefault(require("./MultiQuantitativeTrack"));
-const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
+const CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
 const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
-const XYPlotRenderer_1 = __importDefault(require("./XYPlotRenderer"));
+const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
 const LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
-const LinearWiggleDisplay_1 = __importDefault(require("./LinearWiggleDisplay"));
-const MultiLinearWiggleDisplay_1 = __importDefault(require("./MultiLinearWiggleDisplay"));
-const MultiXYPlotRenderer_1 = __importDefault(require("./MultiXYPlotRenderer"));
-const MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+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 CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
+const MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
 const MultiWiggleAddTrackWorkflow_1 = __importDefault(require("./MultiWiggleAddTrackWorkflow"));
-const utils = __importStar(require("./util"));
+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 LinearWiggleDisplay_2 = require("./LinearWiggleDisplay");
-const XYPlotRenderer_2 = require("./XYPlotRenderer");
+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_2.ReactComponent,
-            XYPlotRendererReactComponent: XYPlotRenderer_2.ReactComponent,
-            XYPlotRenderer: XYPlotRenderer_2.XYPlotRenderer,
+            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_1.ReactComponent,
+            XYPlotRendererReactComponent: XYPlotRenderer_1.ReactComponent,
+            XYPlotRenderer: XYPlotRenderer_1.XYPlotRenderer,
             WiggleBaseRenderer: WiggleBaseRenderer_1.default,
-            linearWiggleDisplayModelFactory: LinearWiggleDisplay_2.modelFactory,
-            xyPlotRendererConfigSchema: XYPlotRenderer_2.configSchema,
+            linearWiggleDisplayModelFactory: LinearWiggleDisplay_1.modelFactory,
+            xyPlotRendererConfigSchema: XYPlotRenderer_1.configSchema,
             utils,
         };
     }
@@ -85,32 +92,7 @@ class WigglePlugin extends Plugin_1.default {
         (0, MultiRowLineRenderer_1.default)(pm);
         (0, MultiWiggleAddTrackWorkflow_1.default)(pm);
         (0, CreateMultiWiggleExtension_1.default)(pm);
-        pm.addToExtensionPoint('Core-guessAdapterForLocation', (cb) => {
-            return (file, index, hint) => {
-                const regexGuess = /\.(bw|bigwig)$/i;
-                const adapterName = 'BigWigAdapter';
-                const fileName = (0, tracks_1.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);
-            };
-        });
+        (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));
@@ -120,9 +102,9 @@ 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_3 = require("./LinearWiggleDisplay");
-Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return LinearWiggleDisplay_3.Tooltip; } });
-Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_3.ReactComponent; } });
-Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_3.modelFactory; } });
+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

@@ -1,4 +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/dist/shared/SetMinMaxDialog.js

@@ -1,32 +1,10 @@
 "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 (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SetMinMaxDialog;
-const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
+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;
@@ -36,21 +14,13 @@ function SetMinMaxDialog(props) {
         ? +max > +min
         : true;
     const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null, "Enter min/max score: "),
-            !ok ? (react_1.default.createElement(material_1.Typography, { color: "error" }, "Max is greater than or equal to min")) : null,
-            !logOk ? (react_1.default.createElement(material_1.Typography, { color: "error" }, "Min score should be greater than 0 for log scale")) : null,
-            react_1.default.createElement(material_1.TextField, { value: min, onChange: event => {
-                    setMin(event.target.value);
-                }, placeholder: "Enter min score" }),
-            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
-                    setMax(event.target.value);
-                }, placeholder: "Enter max score" })),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(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();
-                } }, "Submit"))));
+    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

@@ -1,62 +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/dist/shared/SharedWiggleConfigSchema.js

@@ -4,16 +4,8 @@ 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");
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 function sharedWiggleConfigFactory() {
     return (0, configuration_1.ConfigurationSchema)('SharedWiggleDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
@@ -26,59 +18,38 @@ 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: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            model: mobx_state_tree_1.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: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });