@jbrowse/plugin-wiggle 2.16.1 → 2.18.0

package/esm/index.js

@@ -1,27 +1,24 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { getFileName, } from '@jbrowse/core/util/tracks';
-// locals
-import WiggleBaseRenderer from './WiggleBaseRenderer';
+import { getFileName } from '@jbrowse/core/util/tracks';
 import BigWigAdapterF from './BigWigAdapter';
-import QuantitativeTrackF from './QuantitativeTrack';
-import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
-import MultiWiggleAdapterF from './MultiWiggleAdapter';
+import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
 import DensityRendererF from './DensityRenderer';
-import XYPlotRendererF from './XYPlotRenderer';
 import LinePlotRendererF from './LinePlotRenderer';
-import LinearWiggleDisplayF from './LinearWiggleDisplay';
-import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay';
-import MultiXYPlotRendererF from './MultiXYPlotRenderer';
-import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer';
+import LinearWiggleDisplayF, { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
 import MultiDensityRendererF from './MultiDensityRenderer';
 import MultiLineRendererF from './MultiLineRenderer';
+import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay';
+import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
 import MultiRowLineRendererF from './MultiRowLineRenderer';
-import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
+import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer';
+import MultiWiggleAdapterF from './MultiWiggleAdapter';
 import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
+import MultiXYPlotRendererF from './MultiXYPlotRenderer';
+import QuantitativeTrackF from './QuantitativeTrack';
+import WiggleBaseRenderer from './WiggleBaseRenderer';
+import { MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
+import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from './XYPlotRenderer';
 import * as utils from './util';
-import { WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, MultiWiggleGetSources, } from './WiggleRPC/rpcMethods';
-import { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-import { ReactComponent as XYPlotRendererReactComponent, configSchema as xyPlotRendererConfigSchema, XYPlotRenderer, } from './XYPlotRenderer';
 export default class WigglePlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -86,5 +83,5 @@ export default class WigglePlugin extends Plugin {
 }
 export * from './util';
 export { default as WiggleRendering } from './WiggleRendering';
-export { Tooltip, ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
+export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
 export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';

package/esm/shared/SetMinMaxDialog.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 export default function SetMinMaxDialog(props) {
     const { model, handleClose } = props;
     const { minScore, maxScore, scaleType } = model;

package/{dist/shared/configShared.d.ts → esm/shared/SharedWiggleConfigSchema.d.ts}

@@ -1,62 +1,36 @@
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 export default function sharedWiggleConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     autoscale: {
         type: string;
         defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
     };
-    /**
-     * #slot
-     */
     minimalTicks: {
         type: string;
         defaultValue: boolean;
         description: string;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     numStdDev: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     inverted: {
         type: string;
         description: string;

package/esm/shared/{configShared.js → SharedWiggleConfigSchema.js}

@@ -1,16 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-/**
- * #config SharedWiggleDisplay
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
 export default function sharedWiggleConfigFactory() {
     return ConfigurationSchema('SharedWiggleDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
@@ -23,59 +15,38 @@ export default function sharedWiggleConfigFactory() {
             ]),
             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']), // todo zscale
+            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,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/{dist/shared/modelShared.d.ts → esm/shared/SharedWiggleMixin.d.ts}

@@ -1,8 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
-/**
- * #stateModel SharedWiggleMixin
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export default function SharedWiggleMixin(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>;
@@ -15,21 +12,12 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            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]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -45,9 +33,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 message: React.ReactNode;
                 filled?: boolean;
                 status?: string;
-                reactElement? /**
-                 * #property
-                 */: React.ReactElement;
+                reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -55,15 +41,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -97,64 +77,22 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    /**
-     * #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>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -170,9 +108,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree" /**
-         * #property
-         */).IModelType<{
+        } & import("mobx-state-tree").IStateTreeNode<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>>;
@@ -247,6 +183,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -286,119 +223,42 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
-    /**
-     * #action
-     */
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         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
-     */
+    setStatsLoading(arg?: string): void;
     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 adapterTypeName: any;
-    /**
-     * #getter
-     */
     readonly rendererTypeNameSimple: any;
-    /**
-     * #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 adapterCapabilities: string[];
-    /**
-     * #getter
-     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -407,35 +267,19 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         } & 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" /**
-             * #property
-             */).NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & 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>;
-    /**
-     * #getter
-     */
     readonly autoscaleType: any;
 } & {
-    /**
-     * #getter
-     */
     readonly domain: number[] | undefined;
 } & {
-    /**
-     * #getter
-     */
     readonly filled: boolean;
-    /**
-     * #getter
-     */
     readonly summaryScoreModeSetting: string;
-    /**
-     * #getter
-     */
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -443,26 +287,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         scaleType: any;
         inverted: any;
     };
-    /**
-     * #getter
-     */
     readonly canHaveFill: boolean;
-    /**
-     * #getter
-     */
     readonly displayCrossHatchesSetting: boolean;
-    /**
-     * #getter
-     */
     readonly hasResolution: boolean;
-    /**
-     * #getter
-     */
     readonly hasGlobalStats: boolean;
 } & {
-    /**
-     * #method
-     */
     scoreTrackMenuItems(): ({
         label: string;
         subMenu: {
@@ -485,9 +314,6 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         subMenu?: undefined;
     })[];
 } & {
-    /**
-     * #action
-     */
     reload(): Promise<void>;
 }, {
     type: string;
@@ -503,21 +329,12 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            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]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -533,9 +350,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 message: React.ReactNode;
                 filled?: boolean;
                 status?: string;
-                reactElement? /**
-                 * #property
-                 */: React.ReactElement;
+                reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -543,15 +358,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -585,11 +394,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: string;
     id: string;
+    type: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    heightPreConfig: number | undefined;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;