@jbrowse/plugin-wiggle 2.16.1 → 2.18.0

package/esm/MultiLinearWiggleDisplay/{models/configSchema.d.ts → configSchema.d.ts}

@@ -1,16 +1,10 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
@@ -18,9 +12,6 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     height: {
         type: string;
         defaultValue: number;

package/esm/MultiLinearWiggleDisplay/{models/configSchema.js → configSchema.js}

@@ -1,13 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-// locals
-import sharedWiggleConfigFactory from '../../shared/configShared';
-/**
- * #config MultiLinearWiggleDisplay
- * extends
- * - [SharedWiggleDisplay](../sharedwiggledisplay)
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import sharedWiggleConfigFactory from '../shared/SharedWiggleConfigSchema';
+function x() { }
 export default function WiggleConfigFactory(pluginManager) {
     const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;
     const MultiDensityRendererConfigSchema = pluginManager.getRendererType('MultiDensityRenderer').configSchema;
@@ -15,9 +9,6 @@ export default function WiggleConfigFactory(pluginManager) {
     const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
     const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
     return ConfigurationSchema('MultiLinearWiggleDisplay', {
-        /**
-         * #slot
-         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', [
@@ -29,9 +20,6 @@ export default function WiggleConfigFactory(pluginManager) {
             ]),
             defaultValue: 'multirowxy',
         },
-        /**
-         * #slot
-         */
         renderers: ConfigurationSchema('RenderersConfiguration', {
             MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
             MultiDensityRenderer: MultiDensityRendererConfigSchema,
@@ -39,17 +27,11 @@ export default function WiggleConfigFactory(pluginManager) {
             MultiLineRenderer: MultiLineRendererConfigSchema,
             MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
         }),
-        /**
-         * #slot
-         */
         height: {
             type: 'number',
             defaultValue: 200,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: sharedWiggleConfigFactory(),
         explicitlyTyped: true,
     });

package/esm/MultiLinearWiggleDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MultiLinearWiggleDisplayF(pluginManager: PluginManager): void;

package/esm/MultiLinearWiggleDisplay/index.js

@@ -1,7 +1,7 @@
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import configSchemaFactory from './models/configSchema';
-import modelFactory from './models/model';
 import { lazy } from 'react';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import configSchemaFactory from './configSchema';
+import modelFactory from './model';
 export default function MultiLinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);

package/esm/MultiLinearWiggleDisplay/{models/model.d.ts → model.d.ts}

@@ -1,18 +1,9 @@
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature, AnyReactComponentType } from '@jbrowse/core/util';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
-interface Source {
-    name: string;
-    color?: string;
-    group?: string;
-}
-/**
- * #stateModel MultiLinearWiggleDisplay
- * extends
- * - [SharedWiggleMixin](../sharedwigglemixin)
- */
+import type { Source } from '../util';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { AnyReactComponentType, Feature } from '@jbrowse/core/util';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import type { Instance } from 'mobx-state-tree';
 export 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>;
@@ -25,21 +16,12 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     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;
@@ -63,15 +45,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         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;
@@ -123,13 +99,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
-    /**
-     * #property
-     */
     layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
 }, {
     rendererTypeName: string;
@@ -166,9 +136,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree" /**
-         * #action
-         */).IStateTreeNode<import("mobx-state-tree").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>>;
@@ -222,6 +190,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     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;
 } & {
@@ -261,19 +230,21 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -315,6 +286,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -351,127 +323,54 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     reload(): Promise<void>;
 } & {
+    sourcesLoadingStopToken: string | undefined;
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
 } & {
-    /**
-     * #action
-     */
+    setSourcesLoading(str: string): void;
     setLayout(layout: Source[]): void;
-    /**
-     * #action
-     */
     clearLayout(): void;
-    /**
-     * #action
-     */
     setSources(sources: Source[]): void;
-    /**
-     * #action
-     */
     setFeatureUnderMouse(f?: Feature): void;
 } & {
-    /**
-     * #getter
-     */
     readonly featureUnderMouse: Feature | undefined;
-    /**
-     * #getter
-     */
     readonly TooltipComponent: AnyReactComponentType;
-    /**
-     * #getter
-     */
     readonly rendererTypeName: string;
 } & {
-    /**
-     * #getter
-     */
     readonly needsScalebar: boolean;
-    /**
-     * #getter
-     */
     readonly needsFullHeightScalebar: boolean;
-    /**
-     * #getter
-     */
     readonly isMultiRow: boolean;
-    /**
-     * #getter
-     * can be used to give it a "color scale" like a R heatmap, not
-     * implemented like this yet but flag can be used for this
-     */
     readonly needsCustomLegend: boolean;
     readonly canHaveFill: boolean;
-    /**
-     * #getter
-     * the multirowxy and multiline don't need to use colors on the legend
-     * boxes since their track is drawn with the color. sort of a stylistic
-     * choice
-     */
     readonly renderColorBoxes: boolean;
-    /**
-     * #getter
-     * positions multi-row below the tracklabel even if using overlap
-     * tracklabels for everything else
-     */
     readonly prefersOffset: boolean;
-    /**
-     * #getter
-     */
     readonly sources: {
         color: string;
+        baseUri?: string;
         name: string;
         group?: string;
     }[] | undefined;
+    readonly quantitativeStatsReady: boolean;
 } & {
-    /**
-     * #getter
-     */
     readonly rowHeight: number;
-    /**
-     * #getter
-     */
     readonly rowHeightTooSmallForScalebar: boolean;
-    /**
-     * #getter
-     */
     readonly useMinimalTicks: any;
 } & {
-    /**
-     * #getter
-     */
+    adapterProps(): any;
     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>;
     } | undefined;
-    /**
-     * #getter
-     */
     readonly colors: string[];
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
-    /**
-     * #method
-     */
     renderProps(): any;
-    /**
-     * #getter
-     */
     readonly hasResolution: boolean;
-    /**
-     * #getter
-     */
     readonly hasGlobalStats: boolean;
-    /**
-     * #getter
-     */
-    readonly fillSetting: 2 | 0 | 1;
-} & {
-    /**
-     * #method
-     */
+    readonly fillSetting: 2 | 1 | 0;
+} & {
     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: ({
@@ -518,9 +417,6 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     })[];
 } & {
     afterAttach(): void;
-    /**
-     * #action
-     */
     renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>;