@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/LinearPileupDisplay/model.d.ts

@@ -3,8 +3,18 @@ import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+export interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 /**
  * #stateModel LinearPileupDisplay
+ * #category display
  * extends `BaseLinearDisplay`
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
@@ -13,6 +23,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: 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>;
         region: import("mobx-state-tree").IModelType<{
@@ -31,7 +45,9 @@ 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<any, string | import("react").JSXElementConstructor<any>> | undefined; /**
+         * #property
+         */
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string; /**
@@ -39,8 +55,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
          */
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean;
-        /**
+        maxHeightReached: boolean; /**
          * #property
          */
         ReactComponent: ({ model, }: {
@@ -64,11 +79,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reload(): void;
         beforeDestroy(): void;
     }, 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: {
+            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<"LinearPileupDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -98,7 +134,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     rendererTypeName: string;
-    error: unknown;
+    error: unknown; /**
+     * #action
+     */
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -108,6 +147,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             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]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -115,7 +155,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        /**
+         * #action
+         */
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
     }>;
@@ -125,8 +169,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #action
+             */
             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]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -134,6 +181,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -143,21 +191,52 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number; /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): 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;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    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: Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -171,60 +250,45 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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 estimatedStatsReady: 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;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | 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;
-    reload(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
 } & {
-    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(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: Feature | undefined;
     currSortBpPerPx: number;
-    ready: boolean;
+    modificationsReady: boolean;
+    sortReady: boolean;
+    tagsReady: boolean;
+} & {
+    readonly autorunReady: boolean;
 } & {
     /**
      * #action
      */
-    setReady(flag: boolean): void;
+    setModificationsReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setTagsReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setSortReady(flag: boolean): void;
     /**
      * #action
      */
@@ -260,8 +324,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setFeatureUnderMouse(feat?: Feature): void;
-} & {
-    afterAttach(): void;
     /**
      * #action
      */
@@ -286,30 +348,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setConfig(configuration: AnyConfigurationModel): void;
+    setConfig(conf: AnyConfigurationModel): void;
     /**
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
-    setFilterBy(filter: {
-        flagInclude: number;
-        flagExclude: number;
-        readName?: string;
-        tagFilter?: {
-            tag: string;
-            value: string;
-        };
-    }): void;
+    setFilterBy(filter: Filter): void;
 } & {
     /**
      * #action
      */
     reload(): void;
 } & {
-    /**
-     * #getter
-     */
-    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -318,6 +368,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    /**
+     * #getter
+     */
+    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -330,6 +385,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #getter
      */
     readonly featureUnderMouse: Feature | undefined;
+    /**
+     * #getter
+     */
+    readonly renderReady: boolean;
 } & {
     /**
      * #getter
@@ -352,7 +411,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #getter
      */
-    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => JSX.Element | null;
+    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    /**
+     * #method
+     */
+    renderPropsPre(): any;
     /**
      * #method
      */
@@ -415,6 +478,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         disabled?: undefined;
         subMenu?: undefined;
     })[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -422,12 +487,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    /**
-     * #action
-     */
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
-     * #action
-     */
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: 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>;
         region: import("mobx-state-tree").IModelType<{
@@ -444,9 +508,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #action
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
@@ -458,9 +520,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
-        renderProps: any; /**
-         * #getter
-         */
+        renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
@@ -472,19 +532,39 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any; /**
-             * #getter
-             */
+            renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, 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: {
+            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;