@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/dist/LinearWiggleDisplay/components/Tooltip.js

@@ -10,90 +10,18 @@ var __assign = (this && this.__assign) || function () {
     };
     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;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Tooltip = void 0;
-var react_1 = __importStar(require("react"));
+var react_1 = __importDefault(require("react"));
 var mobx_react_1 = require("mobx-react");
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
 // locals
-var model_1 = require("../models/model");
-var react_popper_1 = require("react-popper");
-// convert to number, apply shortened precision, and render
-function toP(s) {
-    if (s === void 0) { s = 0; }
-    return +(+s).toPrecision(6);
-}
-function round(value) {
-    return Math.round(value * 1e5) / 1e5;
-}
+var Tooltip_1 = __importDefault(require("../../Tooltip"));
+exports.Tooltip = Tooltip_1.default;
+var util_1 = require("../../util");
 var en = function (n) { return n.toLocaleString('en-US'); };
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
-    // these styles come from
-    // https://github.com/mui-org/material-ui/blob/master/packages/material-ui/src/Tooltip/Tooltip.js
-    tooltip: {
-        position: 'absolute',
-        pointerEvents: 'none',
-        backgroundColor: (0, material_1.alpha)(theme.palette.grey[700], 0.9),
-        borderRadius: theme.shape.borderRadius,
-        color: theme.palette.common.white,
-        fontFamily: theme.typography.fontFamily,
-        padding: '4px 8px',
-        fontSize: theme.typography.pxToRem(12),
-        lineHeight: "".concat(round(14 / 10), "em"),
-        maxWidth: 300,
-        wordWrap: 'break-word',
-    },
-    hoverVertical: {
-        background: '#333',
-        border: 'none',
-        width: 1,
-        height: '100%',
-        top: model_1.YSCALEBAR_LABEL_OFFSET,
-        cursor: 'default',
-        position: 'absolute',
-        pointerEvents: 'none',
-    },
-}); });
 var TooltipContents = react_1.default.forwardRef(function (_a, ref) {
     var feature = _a.feature;
     var start = feature.get('start');
@@ -106,57 +34,18 @@ var TooltipContents = react_1.default.forwardRef(function (_a, ref) {
         loc,
         react_1.default.createElement("br", null),
         "Max: ",
-        toP(feature.get('maxScore')),
+        (0, util_1.toP)(feature.get('maxScore')),
         react_1.default.createElement("br", null),
         "Avg: ",
-        toP(feature.get('score')),
+        (0, util_1.toP)(feature.get('score')),
         react_1.default.createElement("br", null),
         "Min: ",
-        toP(feature.get('minScore')))) : (react_1.default.createElement("div", { ref: ref },
+        (0, util_1.toP)(feature.get('minScore')))) : (react_1.default.createElement("div", { ref: ref },
         loc,
-        react_1.default.createElement("br", null), "".concat(toP(feature.get('score')))));
-});
-var Tooltip = (0, mobx_react_1.observer)(function (_a) {
-    var model = _a.model, height = _a.height, clientMouseCoord = _a.clientMouseCoord, offsetMouseCoord = _a.offsetMouseCoord, clientRect = _a.clientRect, TooltipContents = _a.TooltipContents;
-    var featureUnderMouse = model.featureUnderMouse;
-    var _b = __read((0, react_1.useState)(0), 2), width = _b[0], setWidth = _b[1];
-    var _c = __read((0, react_1.useState)(null), 2), anchorEl = _c[0], setAnchorEl = _c[1];
-    var classes = useStyles().classes;
-    // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-    var virtElement = (0, react_1.useMemo)(function () { return ({
-        getBoundingClientRect: function () {
-            var x = clientMouseCoord[0] + width / 2 + 20;
-            var y = (clientRect === null || clientRect === void 0 ? void 0 : clientRect.top) || 0;
-            return {
-                top: y,
-                left: x,
-                bottom: y,
-                right: x,
-                width: 0,
-                height: 0,
-                x: x,
-                y: y,
-                toJSON: function () { },
-            };
-        },
-    }); }, [clientRect === null || clientRect === void 0 ? void 0 : clientRect.top, clientMouseCoord, width]);
-    var _d = (0, react_popper_1.usePopper)(virtElement, anchorEl), styles = _d.styles, attributes = _d.attributes;
-    return featureUnderMouse ? (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Portal, null,
-            react_1.default.createElement("div", __assign({ ref: setAnchorEl, className: classes.tooltip, 
-                // zIndex needed to go over widget drawer
-                style: __assign(__assign({}, styles.popper), { zIndex: 100000 }) }, attributes.popper),
-                react_1.default.createElement(TooltipContents, { ref: function (elt) {
-                        setWidth((elt === null || elt === void 0 ? void 0 : elt.getBoundingClientRect().width) || 0);
-                    }, feature: featureUnderMouse }))),
-        react_1.default.createElement("div", { className: classes.hoverVertical, style: {
-                left: offsetMouseCoord[0],
-                height: height - model_1.YSCALEBAR_LABEL_OFFSET * 2,
-            } }))) : null;
+        react_1.default.createElement("br", null), "".concat((0, util_1.toP)(feature.get('score')))));
 });
-exports.Tooltip = Tooltip;
 var WiggleTooltip = (0, mobx_react_1.observer)(function (props) {
-    return react_1.default.createElement(Tooltip, __assign({ TooltipContents: TooltipContents }, props));
+    return react_1.default.createElement(Tooltip_1.default, __assign({ TooltipContents: TooltipContents }, props));
 });
 exports.default = WiggleTooltip;
 //# sourceMappingURL=Tooltip.js.map

package/dist/LinearWiggleDisplay/components/Tooltip.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;AAAA,gDAAyB;AACzB,yCAAqC;AAGrC,SAAS;AACT,0DAAiE;AAiDxD,kBAjDF,iBAAO,CAiDE;AAhDhB,mCAAgC;AAEhC,IAAM,EAAE,GAAG,UAAC,CAAS,IAAK,OAAA,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,EAAzB,CAAyB,CAAA;AAEnD,IAAM,eAAe,GAAG,eAAK,CAAC,UAAU,CACtC,UAAC,EAAW,EAAE,GAAG;QAAd,OAAO,aAAA;IACR,IAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,IAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,IAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAG,EAAE,CAAC,KAAK,CAAC,eAAK,EAAE,CAAC,GAAG,CAAC,CAAE,CAAC;SACvE,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,CAC5C,uCAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QAClC,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QAC/B,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAC9B,CACP,CAAC,CAAC,CAAC,CACF,uCAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,yCAAM,EACL,UAAG,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAE,CAC3B,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAID,IAAM,aAAa,GAAG,IAAA,qBAAQ,EAC5B,UAAC,KAOA;IACC,OAAO,8BAAC,iBAAO,aAAC,eAAe,EAAE,eAAe,IAAM,KAAK,EAAI,CAAA;AACjE,CAAC,CACF,CAAA;AACD,kBAAe,aAAa,CAAA"}

package/dist/LinearWiggleDisplay/index.d.ts

@@ -1,3 +1,7 @@
-export { default as configSchemaFactory } from './models/configSchema';
-export { default as modelFactory, YSCALEBAR_LABEL_OFFSET } from './models/model';
-export { default as ReactComponent } from './components/WiggleDisplayComponent';
+import PluginManager from '@jbrowse/core/PluginManager';
+import modelFactory from './models/model';
+import ReactComponent from './components/WiggleDisplayComponent';
+import Tooltip from './components/Tooltip';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { ReactComponent, modelFactory, Tooltip };

package/dist/LinearWiggleDisplay/index.js

@@ -3,12 +3,27 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ReactComponent = exports.YSCALEBAR_LABEL_OFFSET = exports.modelFactory = exports.configSchemaFactory = void 0;
-var configSchema_1 = require("./models/configSchema");
-Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
-var model_1 = require("./models/model");
-Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_1).default; } });
-Object.defineProperty(exports, "YSCALEBAR_LABEL_OFFSET", { enumerable: true, get: function () { return model_1.YSCALEBAR_LABEL_OFFSET; } });
-var WiggleDisplayComponent_1 = require("./components/WiggleDisplayComponent");
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(WiggleDisplayComponent_1).default; } });
+exports.Tooltip = exports.modelFactory = exports.ReactComponent = void 0;
+var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+var configSchema_1 = __importDefault(require("./models/configSchema"));
+var model_1 = __importDefault(require("./models/model"));
+exports.modelFactory = model_1.default;
+var WiggleDisplayComponent_1 = __importDefault(require("./components/WiggleDisplayComponent"));
+exports.ReactComponent = WiggleDisplayComponent_1.default;
+var Tooltip_1 = __importDefault(require("./components/Tooltip"));
+exports.Tooltip = Tooltip_1.default;
+exports.default = (function (pluginManager) {
+    pluginManager.addDisplayType(function () {
+        var configSchema = (0, configSchema_1.default)(pluginManager);
+        var stateModel = (0, model_1.default)(pluginManager, configSchema);
+        return new DisplayType_1.default({
+            name: 'LinearWiggleDisplay',
+            configSchema: configSchema,
+            stateModel: stateModel,
+            trackType: 'QuantitativeTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: WiggleDisplayComponent_1.default,
+        });
+    });
+});
 //# sourceMappingURL=index.js.map

package/dist/LinearWiggleDisplay/index.js.map

@@ -1 +1 @@
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package/dist/LinearWiggleDisplay/models/model.d.ts

@@ -3,7 +3,6 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-export declare const YSCALEBAR_LABEL_OFFSET = 5;
 declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -64,6 +63,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -209,7 +209,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats({ scoreMin, scoreMax, }: {
+    updateStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -219,7 +219,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     setLoading(aborter: AbortController): void;
     selectFeature(feature: Feature): void;
     setResolution(res: number): void;
-    setFill(fill: boolean): void;
+    setFill(fill: number): void;
     toggleLogScale(): void;
     setScaleType(scale?: string): void;
     setSummaryScoreMode(val: string): void;
@@ -232,6 +232,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     readonly TooltipComponent: React.FC<{}>;
     readonly adapterTypeName: any;
+    readonly rendererTypeNameSimple: any;
     readonly rendererTypeName: string;
     readonly filters: undefined;
     readonly scaleType: any;
@@ -258,18 +259,36 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly autoscaleType: any;
     readonly displayCrossHatchesSetting: any;
 } & {
-    readonly ticks: any;
+    readonly ticks: {
+        range: number[];
+        values: number[];
+        format: (d: import("d3-scale").NumberValue) => string;
+        position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+    };
+    readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
-    readonly adapterCapabilities: string[];
     readonly hasResolution: boolean;
     readonly hasGlobalStats: boolean;
+    readonly fillSetting: 2 | 1 | 0;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
         type: string;
         label: string;
         checked: any;
         onClick: () => void;
+        subMenu?: undefined;
     })[];
 } & {
     reload(): Promise<void>;