@jbrowse/plugin-wiggle 2.1.6 → 2.2.0

package/esm/LinearWiggleDisplay/models/configSchema.js

@@ -1,11 +1,18 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
+/**
+ * #config LinearWiggleDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export default function WiggleConfigFactory(pluginManager) {
     const XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
     const DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
     const LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
     return ConfigurationSchema('LinearWiggleDisplay', {
+        /**
+         * #slot
+         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
@@ -18,47 +25,77 @@ export default function WiggleConfigFactory(pluginManager) {
             ]),
             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: 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,
         },
+        /**
+         * #slot
+         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),
             defaultValue: 'xyplot',
         },
+        /**
+         * #slot
+         */
         renderers: ConfigurationSchema('RenderersConfiguration', {
             DensityRenderer: DensityRendererConfigSchema,
             XYPlotRenderer: XYPlotRendererConfigSchema,
             LinePlotRenderer: LinePlotRendererConfigSchema,
         }),
-    }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
 }
 //# sourceMappingURL=configSchema.js.map

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

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

@@ -3,7 +3,11 @@ 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';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearWiggleDisplay
+ * Extends `BaseLinearDisplay`
+ */
+declare function 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>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -25,14 +29,20 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        renderInProgress: AbortController | undefined; /**
+         * #property
+         */
         filled: boolean;
         reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
-        layout: any;
+        layout: any; /**
+         * #property
+         */
         status: string;
         error: unknown;
-        message: string | undefined;
+        message: string | undefined; /**
+         * #property
+         */
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
@@ -58,20 +68,65 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
+    /**
+     * #property
+     */
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    /**
+     * #property
+     */
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     */
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
     minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
     displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
         min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -122,11 +177,15 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
+     * #action
+     */
     regionCannotBeRendered(): undefined;
 } & {
     setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
+    setRpcDriverName(rpcDriverName: string): void; /**
+     * #action
+     */
     reload(): void;
 } & {
     currBpPerPx: number;
@@ -170,7 +229,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
     updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
-    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void; /**
+     * #getter
+     */
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
@@ -209,46 +270,143 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     statsFetchInProgress: AbortController | undefined;
 } & {
+    /**
+     * #action
+     */
     updateStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
+    /**
+     * #action
+     */
     setColor(color?: string): void;
+    /**
+     * #action
+     */
     setPosColor(color?: string): void;
+    /**
+     * #action
+     */
     setNegColor(color?: string): void;
+    /**
+     * #action
+     */
     setLoading(aborter: AbortController): void;
+    /**
+     * #action
+     * this overrides the BaseLinearDisplayModel to avoid popping up a
+     * feature detail display, but still sets the feature selection on the
+     * model so listeners can detect a click
+     */
     selectFeature(feature: Feature): void;
+    /**
+     * #action
+     */
     setResolution(res: number): void;
+    /**
+     * #action
+     */
     setFill(fill: number): void;
+    /**
+     * #action
+     */
     toggleLogScale(): void;
+    /**
+     * #action
+     */
     setScaleType(scale?: string): void;
+    /**
+     * #action
+     */
     setSummaryScoreMode(val: string): void;
+    /**
+     * #action
+     */
     setAutoscale(val: string): void;
+    /**
+     * #action
+     */
     setMaxScore(val?: number): void;
+    /**
+     * #action
+     */
     setRendererType(val: string): void;
+    /**
+     * #action
+     */
     setMinScore(val?: number): void;
+    /**
+     * #action
+     */
     toggleCrossHatches(): void;
+    /**
+     * #action
+     */
     setCrossHatches(cross: boolean): void;
 } & {
+    /**
+     * #getter
+     */
     readonly TooltipComponent: React.FC<{}>;
+    /**
+     * #getter
+     */
     readonly adapterTypeName: any;
+    /**
+     * #getter
+     */
     readonly rendererTypeNameSimple: any;
+    /**
+     * #getter
+     */
     readonly rendererTypeName: string;
+    /**
+     * #getter
+     * subclasses can define these, as snpcoverage track does
+     */
     readonly filters: undefined;
+    /**
+     * #getter
+     */
     readonly scaleType: any;
+    /**
+     * #getter
+     */
     readonly maxScore: any;
+    /**
+     * #getter
+     */
     readonly minScore: any;
 } & {
+    /**
+     * #getter
+     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
+    /**
+     * #getter
+     */
     readonly filled: any;
+    /**
+     * #getter
+     */
     readonly summaryScoreModeSetting: any;
+    /**
+     * #getter
+     */
     readonly domain: number[];
+    /**
+     * #getter
+     */
     readonly needsScalebar: boolean;
+    /**
+     * #getter
+     */
     readonly scaleOpts: {
         domain: number[];
         stats: {
@@ -259,23 +417,53 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         scaleType: any;
         inverted: any;
     };
+    /**
+     * #getter
+     */
     readonly canHaveFill: boolean;
+    /**
+     * #getter
+     */
     readonly autoscaleType: any;
+    /**
+     * #getter
+     */
     readonly displayCrossHatchesSetting: any;
 } & {
+    /**
+     * #getter
+     */
     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>;
     };
+    /**
+     * #getter
+     */
     readonly adapterCapabilities: string[];
 } & {
+    /**
+     * #method
+     */
     renderProps(): any;
+    /**
+     * #getter
+     */
     readonly hasResolution: boolean;
+    /**
+     * #getter
+     */
     readonly hasGlobalStats: boolean;
+    /**
+     * #getter
+     */
     readonly fillSetting: 2 | 1 | 0;
 } & {
+    /**
+     * #method
+     */
     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: {
@@ -295,8 +483,15 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         subMenu?: undefined;
     })[];
 } & {
+    /**
+     * #action
+     * re-runs stats and refresh whole display on reload
+     */
     reload(): Promise<void>;
     afterAttach(): void;
+    /**
+     * #action
+     */
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;