@jbrowse/plugin-wiggle 2.4.1 → 2.5.0

package/esm/DensityRenderer/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/LinePlotRenderer/configSchema.d.ts

@@ -1,2 +1,45 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string; /**
+         * #baseConfiguration
+         */
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SetColorDialog({ model, handleClose, }: {
     model: {
         color?: string;

package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { WiggleDisplayModel } from '../models/model';
 declare const LinearWiggleDisplay: (props: {
     model: WiggleDisplayModel;

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

@@ -1,2 +1,99 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function WiggleConfigFactory(pluginManager: PluginManager): 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;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        DensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        XYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        LinePlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

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

@@ -19,9 +19,7 @@ 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]>; /**
-             * #property
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -41,15 +39,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #property
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -59,14 +53,41 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #action
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+     * #property
+     */
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
      * #property
@@ -75,7 +96,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     /**
      * #property
      */
@@ -161,13 +182,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #property
+             */
         } & 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>; /**
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
              * #property
              */
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -192,9 +215,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
+    /**
+     * #property
+     */
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -203,67 +229,54 @@ 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; /**
-     * #action
-     */
+    readonly DisplayMessageComponent: React.FC<any> | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>; /**
-     * #action
-     */
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any; /**
-     * #action
-     */
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    /**
+    readonly featureDensityStatsReady: boolean; /**
      * #getter
      */
-    readonly estimatedStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): 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;
+    clearFeatureDensityStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    reload(): Promise<void>;
+    reload(): Promise<void>; /**
+     * #method
+     */
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -281,7 +294,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -518,9 +531,7 @@ 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]>; /**
-             * #property
-             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -540,15 +551,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #property
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -558,17 +565,45 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #action
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+     * #property
+     */
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;

package/esm/LinearWiggleDisplay/models/model.js

@@ -3,9 +3,9 @@ import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/
 import { getEnv, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
 import { when } from 'mobx';
-import { isAlive, types } from 'mobx-state-tree';
+import { types } from 'mobx-state-tree';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
-import { getNiceDomain, getScale, getStats, statsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
+import { getNiceDomain, getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
 import Tooltip from '../components/Tooltip';
 import YScaleBar from '../../shared/YScaleBar';
 const SetMinMaxDlg = lazy(() => import('../../shared/SetMinMaxDialog'));
@@ -96,7 +96,7 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #action
          */
-        updateStats(stats) {
+        updateQuantitativeStats(stats) {
             const { scoreMin, scoreMax } = stats;
             const EPSILON = 0.000001;
             if (!self.stats) {
@@ -288,8 +288,8 @@ function stateModelFactory(pluginManager, configSchema) {
          * #getter
          */
         get rendererConfig() {
-            const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
-            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, } = self;
+            const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
+            const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
                 ...(scaleType ? { scaleType } : {}),
@@ -312,15 +312,13 @@ function stateModelFactory(pluginManager, configSchema) {
              * #getter
              */
             get filled() {
-                const { fill, rendererConfig: conf } = self;
-                return fill !== null && fill !== void 0 ? fill : readConfObject(conf, 'filled');
+                return readConfObject(self.rendererConfig, 'filled');
             },
             /**
              * #getter
              */
             get summaryScoreModeSetting() {
-                const { summaryScoreMode, rendererConfig: conf } = self;
-                return summaryScoreMode !== null && summaryScoreMode !== void 0 ? summaryScoreMode : readConfObject(conf, 'summaryScoreMode');
+                return readConfObject(self.rendererConfig, 'summaryScoreMode');
             },
             /**
              * #getter
@@ -381,8 +379,7 @@ function stateModelFactory(pluginManager, configSchema) {
              * #getter
              */
             get displayCrossHatchesSetting() {
-                const { displayCrossHatches: hatches, rendererConfig: conf } = self;
-                return hatches !== null && hatches !== void 0 ? hatches : readConfObject(conf, 'displayCrossHatches');
+                return readConfObject(self.rendererConfig, 'displayCrossHatches');
             },
         };
     })
@@ -593,24 +590,10 @@ function stateModelFactory(pluginManager, configSchema) {
              */
             async reload() {
                 self.setError();
-                const aborter = new AbortController();
-                self.setLoading(aborter);
-                try {
-                    const stats = await getStats(self, {
-                        signal: aborter.signal,
-                        ...self.renderProps(),
-                    });
-                    if (isAlive(self)) {
-                        self.updateStats(stats);
-                        superReload();
-                    }
-                }
-                catch (e) {
-                    self.setError(e);
-                }
+                superReload();
             },
             afterAttach() {
-                statsAutorun(self);
+                quantitativeStatsAutorun(self);
             },
             /**
              * #action

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

@@ -1 +1 @@
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