@jbrowse/plugin-wiggle 2.1.7 → 2.2.1

package/esm/LinePlotRenderer/configSchema.js

@@ -1,11 +1,24 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import ConfigSchema from '../configSchema';
+import baseWiggleRendererConfigSchema from '../configSchema';
+/**
+ * #config LinePlotRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = ConfigurationSchema('LinePlotRenderer', {
+    /**
+     * #slot
+     */
     displayCrossHatches: {
         type: 'boolean',
         description: 'choose to draw cross hatches (sideways lines)',
         defaultValue: false,
     },
-}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+});
 export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/esm/LinePlotRenderer/configSchema.js.map

@@ -1 +1 @@
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package/esm/LinearWiggleDisplay/components/Tooltip.d.ts

@@ -4,7 +4,7 @@ import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
 declare const TooltipContents: React.ForwardRefExoticComponent<{
     feature: Feature;
 } & React.RefAttributes<HTMLDivElement>>;
-declare type Coord = [number, number];
+type Coord = [number, number];
 declare const WiggleTooltip: (props: {
     model: {
         featureUnderMouse: Feature;

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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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAClF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,aAA4B;IACtE,MAAM,0BAA0B,GAC9B,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY,CAAA;IAC9D,MAAM,2BAA2B,GAC/B,aAAa,CAAC,eAAe,CAAC,iBAAiB,CAAC,CAAC,YAAY,CAAA;IAC/D,MAAM,4BAA4B,GAChC,aAAa,CAAC,eAAe,CAAC,kBAAkB,CAAC,CAAC,YAAY,CAAA;IAEhE,OAAO,mBAAmB,CACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,OAAO;YACrB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,gBAAgB,EAAE;gBACzC,QAAQ;gBACR,OAAO;gBACP,UAAU;gBACV,SAAS;gBACT,QAAQ;aACT,CAAC;YACF,WAAW,EACT,sFAAsF;SACzF;QAED;;WAEG;QACH,YAAY,EAAE;YACZ,IAAI,EAAE,SAAS;YACf,YAAY,EAAE,KAAK;YACnB,WAAW,EAAE,iCAAiC;SAC/C;QAED;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,MAAM,CAAC,SAAS;YAC9B,WAAW,EAAE,+BAA+B;SAC7C;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,+BAA+B;YAC5C,YAAY,EAAE,MAAM,CAAC,SAAS;SAC/B;QACD;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EACT,8EAA8E;YAChF,YAAY,EAAE,CAAC;SAChB;QACD;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;YACzD,WAAW,EAAE,0BAA0B;YACvC,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,kBAAkB;YAC/B,YAAY,EAAE,KAAK;SACpB;QAED;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;YACpE,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,mBAAmB,CAAC,wBAAwB,EAAE;YACvD,eAAe,EAAE,2BAA2B;YAC5C,cAAc,EAAE,0BAA0B;YAC1C,gBAAgB,EAAE,4BAA4B;SAC/C,CAAC;KACH,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

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

@@ -1,9 +1,13 @@
 import React from 'react';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
 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>>;
@@ -19,7 +23,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
-            setRefName(newRefName: string): void;
+            setRefName(newRefName: string): void; /**
+             * #property
+             */
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -35,12 +41,16 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
+            model: any; /**
+             * #property
+             */
         }) => any;
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void;
+        afterAttach(): void; /**
+         * #property
+         */
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
@@ -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>>;
@@ -125,7 +180,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): undefined;
 } & {
-    setError(error?: unknown): void;
+    setError(error?: unknown): void; /**
+     * #action
+     */
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
@@ -152,7 +209,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
+    readonly maxFeatureScreenDensity: any; /**
+     * #getter
+     */
     readonly estimatedStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
@@ -209,46 +268,143 @@ 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 +415,53 @@ 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;
-    readonly fillSetting: 2 | 1 | 0;
+    /**
+     * #getter
+     */
+    readonly fillSetting: 1 | 2 | 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 +481,15 @@ 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>;
@@ -308,6 +501,6 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
-export declare type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export declare type WiggleDisplayModel = Instance<WiggleDisplayStateModel>;
+export type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type WiggleDisplayModel = Instance<WiggleDisplayStateModel>;
 export default stateModelFactory;