@jbrowse/plugin-wiggle 2.12.0 → 2.12.2

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -11,7 +11,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     private setupPre;
     setup(opts?: BaseOptions): Promise<{
         bigwig: BigWig;
-        header: import("@gmod/bbi").Header;
+        header: Awaited<ReturnType<BigWig["getHeader"]>>;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<string>;

package/dist/BigWigAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BigWigAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BigWigAdapterF(pluginManager) {
@@ -41,4 +42,3 @@ function BigWigAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigWigAdapter'))).then(r => r.default),
     }));
 }
-exports.default = BigWigAdapterF;

package/dist/CreateMultiWiggleExtension/index.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = CreateMultiWiggleExtensionF;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
@@ -82,4 +83,3 @@ function CreateMultiWiggleExtensionF(pm) {
         ];
     });
 }
-exports.default = CreateMultiWiggleExtensionF;

package/dist/DensityRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = DensityRendererF;
 const configSchema_1 = __importDefault(require("./configSchema"));
 const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
 const WiggleRendering_1 = __importDefault(require("../WiggleRendering"));
@@ -14,4 +15,3 @@ function DensityRendererF(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = DensityRendererF;

package/dist/LinePlotRenderer/configSchema.d.ts

@@ -11,9 +11,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
     color: {
         type: string;
         description: string;
-        defaultValue: string; /**
-         * #baseConfiguration
-         */
+        defaultValue: string;
     };
     posColor: {
         type: string;

package/dist/LinePlotRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinePlotRendererF;
 const configSchema_1 = __importDefault(require("./configSchema"));
 const WiggleRendering_1 = __importDefault(require("../WiggleRendering"));
 const LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
@@ -14,4 +15,3 @@ function LinePlotRendererF(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = LinePlotRendererF;

package/dist/LinearWiggleDisplay/index.js

@@ -27,6 +27,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.modelFactory = exports.ReactComponent = exports.Tooltip = void 0;
+exports.default = LinearWiggleDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
@@ -46,7 +47,6 @@ function LinearWiggleDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearWiggleDisplayF;
 var Tooltip_1 = require("./components/Tooltip");
 Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
 var WiggleDisplayComponent_1 = require("./components/WiggleDisplayComponent");

package/dist/LinearWiggleDisplay/models/configSchema.d.ts

@@ -69,9 +69,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    }; /**
-     * #slot
-     */
+    };
     height: {
         type: string;
         defaultValue: number;

package/dist/LinearWiggleDisplay/models/configSchema.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = WiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
@@ -41,4 +42,3 @@ function WiggleConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = WiggleConfigFactory;

package/dist/LinearWiggleDisplay/models/model.d.ts

@@ -24,7 +24,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree" /**
+             * #getter
+             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -36,7 +38,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -45,25 +47,25 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error?: unknown;
+                error? /**
+                 * #getter
+                 */: unknown;
                 reload: () => void;
                 message: React.ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
             };
         }) => React.JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
-         * #method
-         */
+        setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            reactElement: React.ReactElement;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -134,7 +136,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import(
+        /**
+         * #stateModel LinearWiggleDisplay
+         * extends
+         * - [SharedWiggleMixin](../sharedwigglemixin)
+         */
+        "mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
@@ -146,9 +154,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
+         * #getter
+         */)._NotCustomized>>;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -171,16 +181,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -193,8 +201,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -206,12 +214,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void; /**
-     * #method
-     */
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -220,8 +226,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -229,7 +235,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly renderDelay: number;
     readonly TooltipComponent: React.FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -242,8 +248,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -254,31 +260,31 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     renderSvg(opts: ExportSvgDisplayOptions): Promise<React.JSX.Element>;
     afterAttach(): void;
 } & {
-    message: string | undefined;
+    message: undefined | string;
     stats: {
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: AbortController | undefined;
+    statsFetchInProgress: undefined | AbortController;
 } & {
     updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
-    setColor(color?: string | undefined): void;
-    setPosColor(color?: string | undefined): void;
-    setNegColor(color?: string | undefined): void;
+    setColor(color?: string): void;
+    setPosColor(color?: string): void;
+    setNegColor(color?: string): void;
     setLoading(aborter: AbortController): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
     toggleLogScale(): void;
-    setScaleType(scale?: string | undefined): void;
+    setScaleType(scale?: string): void;
     setSummaryScoreMode(val: string): void;
     setAutoscale(val: string): void;
-    setMaxScore(val?: number | undefined): void;
+    setMaxScore(val?: number): void;
     setRendererType(val: string): void;
-    setMinScore(val?: number | undefined): void;
+    setMinScore(val?: number): void;
     toggleCrossHatches(): void;
     setCrossHatches(cross: boolean): void;
 } & {
@@ -293,7 +299,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     readonly autoscaleType: any;
 } & {
@@ -343,7 +355,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly TooltipComponent: React.FC<{}>;
+    readonly TooltipComponent: React.FC;
     /**
      * #getter
      */

package/dist/LinearWiggleDisplay/models/renderSvg.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSvg = void 0;
+exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
@@ -17,4 +17,3 @@ async function renderSvg(self, opts, superRenderSvg) {
         needsScalebar && stats ? (react_1.default.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
             react_1.default.createElement(YScaleBar_1.default, { model: self, orientation: "left" }))) : null));
 }
-exports.renderSvg = renderSvg;

package/dist/MultiDensityRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MultiDensityRendererF;
 const configSchema_1 = __importDefault(require("./configSchema"));
 const MultiWiggleRendering_1 = __importDefault(require("../MultiWiggleRendering"));
 const MultiDensityRenderer_1 = __importDefault(require("./MultiDensityRenderer"));
@@ -14,4 +15,3 @@ function MultiDensityRendererF(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = MultiDensityRendererF;

package/dist/MultiLineRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MultiLineRendererF;
 const MultiWiggleRendering_1 = __importDefault(require("../MultiWiggleRendering"));
 const MultiLineRenderer_1 = __importDefault(require("./MultiLineRenderer"));
 const configSchema_1 = __importDefault(require("./configSchema"));
@@ -14,4 +15,3 @@ function MultiLineRendererF(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = MultiLineRendererF;

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SetColorDialog;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
@@ -73,4 +74,3 @@ function SetColorDialog({ model, handleClose, }) {
                     handleClose();
                 } }, "Submit"))));
 }
-exports.default = SetColorDialog;

package/dist/MultiLinearWiggleDisplay/components/util.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getOffset = exports.moveDown = exports.moveUp = void 0;
+exports.moveUp = moveUp;
+exports.moveDown = moveDown;
+exports.getOffset = getOffset;
 const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
 function moveUp(arr, sel, by = 1) {
@@ -17,7 +19,6 @@ function moveUp(arr, sel, by = 1) {
     }
     return arr;
 }
-exports.moveUp = moveUp;
 function moveDown(arr, sel, by = 1) {
     const idxs = sel
         .map(l => arr.findIndex(v => v.name === l))
@@ -32,7 +33,6 @@ function moveDown(arr, sel, by = 1) {
     }
     return arr;
 }
-exports.moveDown = moveDown;
 const trackLabelFontSize = 12.8;
 function getOffset(model) {
     const { prefersOffset } = model;
@@ -43,4 +43,3 @@ function getOffset(model) {
         ? (0, util_1.measureText)(trackName, trackLabelFontSize) + 100
         : 10;
 }
-exports.getOffset = getOffset;

package/dist/MultiLinearWiggleDisplay/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MultiLinearWiggleDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
@@ -44,4 +45,3 @@ function MultiLinearWiggleDisplayF(pluginManager) {
         });
     });
 }
-exports.default = MultiLinearWiggleDisplayF;

package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts

@@ -78,9 +78,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    }; /**
-     * #slot
-     */
+    };
     mouseover: {
         type: string;
         description: string;

package/dist/MultiLinearWiggleDisplay/models/configSchema.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = WiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
@@ -59,4 +60,3 @@ function WiggleConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = WiggleConfigFactory;