@jbrowse/plugin-alignments 2.12.0 → 2.12.2

package/esm/LinearPileupDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
@@ -25,7 +24,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             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>;
+            assemblyName: import("mobx-state-tree" /**
+             * #property
+             */).ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -35,7 +36,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -47,9 +48,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement? /**
+                 * #property
+                 */: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -60,7 +63,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -107,9 +110,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>; /**
-         * #action
-         */
+        extra: import("mobx-state-tree").IType<any, any, any>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -156,8 +157,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -167,9 +168,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #action
-             */
+            message: string | undefined;
         } & 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>;
@@ -178,18 +177,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
+         * #action
+         */)._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -202,8 +203,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -215,10 +216,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): 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;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -227,8 +228,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -236,7 +237,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -249,8 +250,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -262,38 +263,40 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined; /**
-     * #action
-     */
+    featureUnderMouseVolatile: undefined | import("@jbrowse/core/util").Feature;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n: number): void;
-    setFeatureHeight(n?: number | undefined): void;
-    setNoSpacing(flag?: boolean | undefined): void;
+    setFeatureHeight(n?: number): void;
+    setNoSpacing(flag?: boolean): void;
     setColorScheme(colorScheme: {
         type: string;
-        tag?: string | undefined;
-        extra?: import("../shared/color").ExtraColorBy | undefined;
+        tag?: string;
+        extra?: import("../shared/color").ExtraColorBy;
     }): void;
     updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
-    setConfig(conf: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
+    setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("../shared").IFilter): void;
     setJexlFilters(filters: string[]): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & 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").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree" /**
+         * #property
+         */).IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly maxHeight: any;
@@ -320,8 +323,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 pos: number;
                 refName: number;
                 type: string;
-                tag?: string | undefined;
-            } | undefined;
+                tag?: string;
+            };
         };
     }) => import("react").JSX.Element | null;
     renderPropsPre(): any;
@@ -396,7 +399,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & 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").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -30,9 +30,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").ISimpleType<string>; /**
-             * #property
-             */
+            value: import("mobx-state-tree").ISimpleType<string>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -61,16 +59,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & 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>>; /**
-             * #property
-             */
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -82,9 +78,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #action
-             */
+            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>>;
         }, {
@@ -97,12 +91,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -115,14 +109,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number; /**
-     * #property
-     */
+    readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
     readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
@@ -130,10 +122,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): 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;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;

package/esm/LinearReadCloudDisplay/configSchema.d.ts

@@ -33,9 +33,6 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     maxFeatureScreenDensity: {
         type: string;
         description: string;
-        /**
-         * #slot
-         */
         defaultValue: number;
     };
     fetchSizeLimit: {

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -44,14 +44,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
-        /**
-         * #stateModel LinearReadCloudDisplay
-         * it is not a block based track, hence not BaseLinearDisplay
-         * extends
-         * - [BaseDisplay](../basedisplay)
-         * - [TrackHeightMixin](../trackheightmixin)
-         * - [FeatureDensityMixin](../featuredensitymixin)
-         */
         model: {
             id: string;
             type: string;
@@ -61,16 +53,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree" /**
+             * #property
+             */).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>>;
+            rpcDriverName: import("mobx-state-tree" /**
+             * #property
+             */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -83,28 +79,26 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             message: string | undefined;
         } & 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>; /**
-             * #action
-             * internal, a reference to a HTMLCanvas because we use a autorun to draw
-             * the canvas
-             */
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree" /**
+         * #action
+         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -117,8 +111,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -130,10 +124,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): 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;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import PluginManager from '@jbrowse/core/PluginManager';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
@@ -34,7 +33,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -45,12 +44,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode; /**
-                 * #property
-                 */
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                message: import("react").ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -61,7 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -92,14 +89,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             description: string;
             defaultValue: string;
             contextVariable: string[];
-        }; /**
-         * #property
-         */
+        };
         jexlFilters: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
@@ -146,9 +139,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
-         * #property
-         */
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
             value: import("mobx-state-tree").ISimpleType<string>;

package/esm/MismatchParser/index.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Feature } from '@jbrowse/core/util';
 export interface Mismatch {
     qual?: number;

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Feature, Region } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
@@ -42,8 +41,8 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         canvasRecordedData: any;
-        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        html?: string | undefined;
+        reactElement?: import("react").ReactElement;
+        html?: string;
     } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
@@ -51,7 +50,7 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         reactElement: import("react").JSX.Element;
-        html?: string | undefined;
+        html?: string;
     } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
@@ -59,8 +58,8 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         imageData: any;
-        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        html?: string | undefined;
+        reactElement?: import("react").ReactElement;
+        html?: string;
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }

package/esm/util.d.ts

@@ -17,7 +17,7 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): boolean;
+export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
 export declare const modificationColors: Record<string, string | undefined>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.12.0",
+  "version": "2.12.2",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
+  "gitHead": "1ec66736ce048a1637f52b7a7ef2eb02d956b771"
 }