@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -0,0 +1,244 @@
+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var util_1 = require("@jbrowse/core/util");
+var rxjs_2 = require("rxjs");
+var operators_1 = require("rxjs/operators");
+function getFilename(uri) {
+    var filename = uri.slice(uri.lastIndexOf('/') + 1);
+    return filename.slice(0, filename.lastIndexOf('.'));
+}
+var MultiWiggleAdapter = /** @class */ (function (_super) {
+    __extends(MultiWiggleAdapter, _super);
+    function MultiWiggleAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    MultiWiggleAdapter.prototype.getAdapters = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var getSubAdapter, subConfs, entries;
+            var _this = this;
+            return __generator(this, function (_a) {
+                getSubAdapter = this.getSubAdapter;
+                if (!getSubAdapter) {
+                    throw new Error('no getSubAdapter available');
+                }
+                subConfs = this.getConf('subadapters');
+                if (!(subConfs === null || subConfs === void 0 ? void 0 : subConfs.length)) {
+                    entries = this.getConf('bigWigs');
+                    subConfs = entries.map(function (entry) { return ({
+                        type: 'BigWigAdapter',
+                        source: getFilename(entry),
+                        bigWigLocation: {
+                            uri: entry,
+                        },
+                    }); });
+                }
+                return [2 /*return*/, Promise.all(
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    subConfs.map(function (conf) { return __awaiter(_this, void 0, void 0, function () {
+                        var dataAdapter;
+                        return __generator(this, function (_a) {
+                            switch (_a.label) {
+                                case 0: return [4 /*yield*/, getSubAdapter(conf)];
+                                case 1:
+                                    dataAdapter = (_a.sent())
+                                        .dataAdapter;
+                                    return [2 /*return*/, __assign(__assign({ source: dataAdapter.id }, conf), { dataAdapter: dataAdapter })];
+                            }
+                        });
+                    }); }))];
+            });
+        });
+    };
+    // note: can't really have dis-agreeing refNames
+    MultiWiggleAdapter.prototype.getRefNames = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var adapters;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getAdapters()];
+                    case 1:
+                        adapters = _a.sent();
+                        return [2 /*return*/, adapters[0].dataAdapter.getRefNames(opts)];
+                }
+            });
+        });
+    };
+    MultiWiggleAdapter.prototype.getGlobalStats = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var adapters, stats, scoreMin, scoreMax;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getAdapters()];
+                    case 1:
+                        adapters = _a.sent();
+                        return [4 /*yield*/, Promise.all(
+                            // @ts-ignore
+                            adapters.map(function (adp) { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))];
+                    case 2:
+                        stats = (_a.sent()).filter(function (f) { return !!f; });
+                        scoreMin = Math.min.apply(Math, __spreadArray([], __read(stats.map(function (s) { return s.scoreMin; })), false));
+                        scoreMax = Math.max.apply(Math, __spreadArray([], __read(stats.map(function (s) { return s.scoreMax; })), false));
+                        return [2 /*return*/, { scoreMin: scoreMin, scoreMax: scoreMax }];
+                }
+            });
+        });
+    };
+    MultiWiggleAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var adapters;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getAdapters()];
+                    case 1:
+                        adapters = _a.sent();
+                        rxjs_2.merge.apply(void 0, __spreadArray([], __read(adapters.map(function (adp) {
+                            return adp.dataAdapter.getFeatures(region, opts).pipe((0, operators_1.map)(function (p) {
+                                // add source field if it does not exist
+                                return p.get('source')
+                                    ? p
+                                    : new util_1.SimpleFeature(__assign(__assign({}, p.toJSON()), { uniqueId: adp.source + '-' + p.id(), source: adp.source }));
+                            }));
+                        })), false)).subscribe(observer);
+                        return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    // always render bigwig instead of calculating a feature density for it
+    MultiWiggleAdapter.prototype.estimateRegionsStats = function (_regions) {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, { featureDensity: 0 }];
+            });
+        });
+    };
+    // in another adapter type, this could be dynamic depending on region or
+    // something, but it is static for this particular multi-wiggle adapter type
+    MultiWiggleAdapter.prototype.getSources = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var adapters;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getAdapters()];
+                    case 1:
+                        adapters = _a.sent();
+                        return [2 /*return*/, adapters.map(function (_a) {
+                                var dataAdapter = _a.dataAdapter, source = _a.source, rest = __rest(_a, ["dataAdapter", "source"]);
+                                return (__assign({ name: source }, rest));
+                            })];
+                }
+            });
+        });
+    };
+    MultiWiggleAdapter.prototype.freeResources = function () { };
+    MultiWiggleAdapter.capabilities = [
+        'hasResolution',
+        'hasLocalStats',
+        'hasGlobalStats',
+    ];
+    return MultiWiggleAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = MultiWiggleAdapter;
+//# sourceMappingURL=MultiWiggleAdapter.js.map

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MultiWiggleAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/MultiWiggleAdapter/configSchema.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('MultiWiggleAdapter', {
+    subadapters: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    bigWigs: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/MultiWiggleAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/MultiWiggleAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/MultiWiggleAdapter/index.js

@@ -0,0 +1,47 @@
+"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;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configSchema_1 = __importDefault(require("./configSchema"));
+var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+exports.default = (function (pluginManager) {
+    pluginManager.addAdapterType(function () {
+        return new AdapterType_1.default({
+            name: 'MultiWiggleAdapter',
+            configSchema: configSchema_1.default,
+            adapterCapabilities: [
+                'hasResolution',
+                'hasLocalStats',
+                'hasGlobalStats',
+            ],
+            getAdapterClass: function () {
+                return Promise.resolve().then(function () { return __importStar(require('./MultiWiggleAdapter')); }).then(function (r) { return r.default; });
+            },
+        });
+    });
+});
+//# sourceMappingURL=index.js.map

package/dist/MultiWiggleAdapter/index.js.map

@@ -0,0 +1 @@
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package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+import { AddTrackModel } from '@jbrowse/plugin-data-management';
+export default function MultiWiggleWidget({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;

package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js

@@ -0,0 +1,139 @@
+"use strict";
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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;
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var util_1 = require("@jbrowse/core/util");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+    textbox: {
+        width: '100%',
+    },
+    paper: {
+        margin: theme.spacing(),
+        padding: theme.spacing(),
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+}); });
+function MultiWiggleWidget(_a) {
+    var model = _a.model;
+    var classes = useStyles().classes;
+    var _b = __read((0, react_1.useState)(''), 2), val = _b[0], setVal = _b[1];
+    var _c = __read((0, react_1.useState)('MultiWiggle ' + Date.now()), 2), trackName = _c[0], setTrackName = _c[1];
+    return (react_1.default.createElement(material_1.Paper, { className: classes.paper },
+        react_1.default.createElement("ul", null,
+            react_1.default.createElement("li", null, "Enter list of URLs for bigwig files in the textbox"),
+            react_1.default.createElement("li", null, "Or, use the button below the text box to select files from your computer")),
+        react_1.default.createElement(material_1.TextField, { multiline: true, rows: 10, value: val, onChange: function (event) { return setVal(event.target.value); }, placeholder: 'Paste list of URLs here, or use file selector below', variant: "outlined", className: classes.textbox }),
+        react_1.default.createElement(material_1.Button, { variant: "outlined", component: "label" },
+            "Choose Files from your computer",
+            react_1.default.createElement("input", { type: "file", hidden: true, multiple: true, onChange: function (_a) {
+                    var target = _a.target;
+                    var res = Array.from((target === null || target === void 0 ? void 0 : target.files) || []).map(function (file) { return ({
+                        type: 'BigWigAdapter',
+                        bigWigLocation: util_1.isElectron
+                            ? {
+                                localPath: file.path,
+                                locationType: 'LocalPathLocation',
+                            }
+                            : (0, tracks_1.storeBlobLocation)({ blob: file }),
+                        source: file.name,
+                    }); });
+                    setVal(JSON.stringify(res, null, 2));
+                } })),
+        react_1.default.createElement(material_1.TextField, { value: trackName, onChange: function (event) { return setTrackName(event.target.value); }, helperText: "Track name" }),
+        react_1.default.createElement(material_1.Button, { variant: "contained", className: classes.submit, onClick: function () {
+                var _a;
+                var session = (0, util_1.getSession)(model);
+                var trackId = [
+                    "".concat(trackName.toLowerCase().replace(/ /g, '_'), "-").concat(Date.now()),
+                    "".concat(session.adminMode ? '' : '-sessionTrack'),
+                ].join('');
+                // allow list of bigwigs in JSON format or line-by-line
+                var bigWigs;
+                try {
+                    bigWigs = JSON.parse(val);
+                }
+                catch (e) {
+                    bigWigs = val.split('\n');
+                }
+                var obj = typeof bigWigs[0] === 'string'
+                    ? { bigWigs: bigWigs }
+                    : { subadapters: bigWigs };
+                session.addTrackConf({
+                    trackId: trackId,
+                    type: 'MultiQuantitativeTrack',
+                    name: trackName,
+                    assemblyNames: [model.assembly],
+                    adapter: __assign({ type: 'MultiWiggleAdapter' }, obj),
+                });
+                (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
+                model.clearData();
+                session.hideWidget(model);
+            } }, "Submit"),
+        react_1.default.createElement("p", null, "Additional notes: "),
+        react_1.default.createElement("ul", null,
+            react_1.default.createElement("li", null,
+                "The list of bigwig files in the text box can be a list of URLs, or a list of elements like",
+                ' ',
+                react_1.default.createElement("code", null, "[{\"type\":\"BigWigAdapter\",\"bigWigLocation\":{\"uri\":\"http://host/file.bw\"}, \"color\":\"green\",\"source\":\"name for subtrack\"}]"),
+                ' ',
+                "to apply e.g. the color attribute to the view"),
+            react_1.default.createElement("li", null, "Adding local files will update the textbox with JSON contents that are ready to submit with the \"Submit\" button"))));
+}
+exports.default = MultiWiggleWidget;
+//# sourceMappingURL=AddTrackWorkflow.js.map

package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map

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package/dist/MultiWiggleAddTrackWidget/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pm: PluginManager) => void;
+export default _default;

package/dist/MultiWiggleAddTrackWidget/index.js

@@ -0,0 +1,19 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+var mobx_state_tree_1 = require("mobx-state-tree");
+// locals
+var AddTrackWorkflow_1 = __importDefault(require("./AddTrackWorkflow"));
+exports.default = (function (pm) {
+    pm.addAddTrackWorkflowType(function () {
+        return new pluggableElementTypes_1.AddTrackWorkflowType({
+            name: 'Multi-wiggle track',
+            ReactComponent: AddTrackWorkflow_1.default,
+            stateModel: mobx_state_tree_1.types.model({}),
+        });
+    });
+});
+//# sourceMappingURL=index.js.map

package/dist/MultiWiggleAddTrackWidget/index.js.map

@@ -0,0 +1 @@
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package/dist/MultiWiggleRendering.d.ts

@@ -0,0 +1,21 @@
+/// <reference types="react" />
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
+import { Source } from './util';
+declare function WiggleRendering(props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    onMouseLeave: Function;
+    onMouseMove: Function;
+    onFeatureClick: Function;
+    blockKey: string;
+    sources: Source[];
+    displayModel: {
+        isMultiRow: boolean;
+    };
+}): JSX.Element;
+declare const _default: typeof WiggleRendering;
+export default _default;