@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/dist/LinearWiggleDisplay/index.js

@@ -1,43 +1,29 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+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,
+        });
+    });
 });
-Object.defineProperty(exports, "ReactComponent", {
-  enumerable: true,
-  get: function get() {
-    return _WiggleDisplayComponent.default;
-  }
-});
-Object.defineProperty(exports, "YSCALEBAR_LABEL_OFFSET", {
-  enumerable: true,
-  get: function get() {
-    return _model.YSCALEBAR_LABEL_OFFSET;
-  }
-});
-Object.defineProperty(exports, "configSchemaFactory", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-Object.defineProperty(exports, "modelFactory", {
-  enumerable: true,
-  get: function get() {
-    return _model.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./models/configSchema"));
-
-var _model = _interopRequireWildcard(require("./models/model"));
-
-var _WiggleDisplayComponent = _interopRequireDefault(require("./components/WiggleDisplayComponent"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+//# sourceMappingURL=index.js.map

package/dist/LinearWiggleDisplay/index.js.map

@@ -0,0 +1 @@
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package/dist/LinearWiggleDisplay/models/configSchema.js

@@ -1,71 +1,67 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = WiggleConfigFactory;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _mobxStateTree = require("mobx-state-tree");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+var mobx_state_tree_1 = require("mobx-state-tree");
 function WiggleConfigFactory(pluginManager) {
-  var XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
-  var DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
-  var LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
-  return (0, _configuration.ConfigurationSchema)('LinearWiggleDisplay', {
-    autoscale: {
-      type: 'stringEnum',
-      defaultValue: 'local',
-      model: _mobxStateTree.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: _mobxStateTree.types.enumeration('Scale type', ['linear', 'log']),
-      // todo zscale
-      description: 'The type of scale to use',
-      defaultValue: 'linear'
-    },
-    inverted: {
-      type: 'boolean',
-      description: 'draw upside down',
-      defaultValue: false
-    },
-    defaultRendering: {
-      type: 'stringEnum',
-      model: _mobxStateTree.types.enumeration('Rendering', ['density', 'xyplot', 'line']),
-      defaultValue: 'xyplot'
-    },
-    renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
-      DensityRenderer: DensityRendererConfigSchema,
-      XYPlotRenderer: XYPlotRendererConfigSchema,
-      LinePlotRenderer: LinePlotRendererConfigSchema
-    })
-  }, {
-    baseConfiguration: _pluginLinearGenomeView.baseLinearDisplayConfigSchema,
-    explicitlyTyped: true
-  });
-}
+    var XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
+    var DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
+    var LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
+    return (0, configuration_1.ConfigurationSchema)('LinearWiggleDisplay', {
+        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,
+        },
+        defaultRendering: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Rendering', ['density', 'xyplot', 'line']),
+            defaultValue: 'xyplot',
+        },
+        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
+            DensityRenderer: DensityRendererConfigSchema,
+            XYPlotRenderer: XYPlotRendererConfigSchema,
+            LinePlotRenderer: LinePlotRendererConfigSchema,
+        }),
+    }, { baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema, explicitlyTyped: true });
+}
+exports.default = WiggleConfigFactory;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearWiggleDisplay/models/configSchema.js.map

@@ -0,0 +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>>;
@@ -81,11 +81,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     error: unknown;
 } & {
     readonly RenderingComponent: React.FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -100,11 +100,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: React.FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -190,7 +190,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         onClick: () => void;
     }[];
     renderProps(): any;
@@ -207,7 +209,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats({ scoreMin, scoreMax, }: {
+    updateStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -217,7 +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;
@@ -230,6 +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;
@@ -256,18 +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>;
@@ -276,10 +297,10 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         overrideHeight: number;
     }): Promise<JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, {
-    id: string;
     type: string;
-    rpcDriverName: string | undefined;
     height: number;
+    id: string;
+    rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;