@jbrowse/plugin-sequence 2.4.2 → 2.5.0

package/dist/BgzipFastaAdapter/configSchema.d.ts

@@ -1,2 +1,44 @@
-declare const BgzipFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    faiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: string;
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    gziLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BgzipFastaAdapter;

package/dist/ChromSizesAdapter/configSchema.d.ts

@@ -1,2 +1,13 @@
-declare const ChromSizesAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    chromSizesLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default ChromSizesAdapter;

package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Feature, Region } from '@jbrowse/core/util';
 declare function Sequence(props: {

package/dist/DivSequenceRenderer/configSchema.d.ts

@@ -1,2 +1,11 @@
-declare const DivSequenceRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default DivSequenceRenderer;

package/dist/IndexedFastaAdapter/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const IndexedFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    faiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: string;
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default IndexedFastaAdapter;

package/dist/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -1 +1,12 @@
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        height: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -9,6 +9,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
+    /**
+     * #getter
+     */
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
@@ -44,9 +47,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #action
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
@@ -63,9 +64,35 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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: {
+            /**
+             * #property
+             */
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showForward: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showReverse: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showTranslation: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -127,8 +154,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: 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";
@@ -147,26 +174,26 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
 } & {
     afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): 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 | undefined): 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: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
@@ -232,6 +259,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
+    /**
+     * #getter
+     */
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
@@ -267,9 +297,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #action
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
@@ -286,9 +314,36 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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: {
+            /**
+             * #property
+             */
+            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/dist/ReferenceSequenceTrack/configSchema.d.ts

@@ -1,2 +1,47 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * configuration for track adapter
+     */
+    adapter: import("mobx-state-tree").IAnyModelType;
+    /**
+     * #slot
+     * configuration for the displays e.g. LinearReferenceSequenceDisplay
+     */
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     */
+    name: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot formatAbout.config
+         */
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        /**
+         * #slot formatAbout.hideUris
+         */
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;

package/dist/SequenceSearchAdapter/configSchema.d.ts

@@ -1,2 +1,39 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    search: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+        type: string;
+        defaultValue: null;
+    };
+    /**
+     * #slot
+     */
+    searchForward: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    searchReverse: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    caseInsensitive: {
+        type: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,7 +1,7 @@
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class TwoBitAdapter extends BaseSequenceAdapter {

package/dist/TwoBitAdapter/configSchema.d.ts

@@ -1,2 +1,24 @@
-declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    twoBitLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    chromSizesLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default TwoBitAdapter;

package/esm/BgzipFastaAdapter/configSchema.d.ts

@@ -1,2 +1,44 @@
-declare const BgzipFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    faiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: string;
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    gziLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BgzipFastaAdapter;

package/esm/ChromSizesAdapter/configSchema.d.ts

@@ -1,2 +1,13 @@
-declare const ChromSizesAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    chromSizesLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default ChromSizesAdapter;

package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Feature, Region } from '@jbrowse/core/util';
 declare function Sequence(props: {

package/esm/DivSequenceRenderer/configSchema.d.ts

@@ -1,2 +1,11 @@
-declare const DivSequenceRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default DivSequenceRenderer;

package/esm/IndexedFastaAdapter/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const IndexedFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    faiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: string;
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default IndexedFastaAdapter;

package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -1 +1,12 @@
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        height: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -9,6 +9,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
+    /**
+     * #getter
+     */
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
@@ -44,9 +47,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #action
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
@@ -63,9 +64,35 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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: {
+            /**
+             * #property
+             */
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showForward: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showReverse: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showTranslation: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -127,8 +154,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: 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";
@@ -147,26 +174,26 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
 } & {
     afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): 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 | undefined): 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: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
@@ -232,6 +259,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
+    /**
+     * #getter
+     */
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
@@ -267,9 +297,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #action
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
@@ -286,9 +314,36 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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: {
+            /**
+             * #property
+             */
+            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/ReferenceSequenceTrack/configSchema.d.ts

@@ -1,2 +1,47 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * configuration for track adapter
+     */
+    adapter: import("mobx-state-tree").IAnyModelType;
+    /**
+     * #slot
+     * configuration for the displays e.g. LinearReferenceSequenceDisplay
+     */
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     */
+    name: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot formatAbout.config
+         */
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        /**
+         * #slot formatAbout.hideUris
+         */
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;

package/esm/SequenceSearchAdapter/configSchema.d.ts

@@ -1,2 +1,39 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    search: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+        type: string;
+        defaultValue: null;
+    };
+    /**
+     * #slot
+     */
+    searchForward: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    searchReverse: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    caseInsensitive: {
+        type: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,7 +1,7 @@
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class TwoBitAdapter extends BaseSequenceAdapter {

package/esm/TwoBitAdapter/configSchema.d.ts

@@ -1,2 +1,24 @@
-declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    twoBitLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    chromSizesLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default TwoBitAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.4.2",
+  "version": "2.5.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }

package/src/TwoBitAdapter/TwoBitAdapter.ts

@@ -5,7 +5,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TwoBitFile } from '@gmod/twobit'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'