@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -13,7 +13,7 @@ interface Filter {
 }
 /**
  * #stateModel LinearReadCloudDisplay
- * extends `BaseLinearDisplay`
+ * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -21,93 +21,12 @@ 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>>;
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>; /**
-         * #property
-         */
-        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>;
-        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;
-        filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: any; /**
-             * #action
-             */
-        }) => any;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            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">>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
-    /**
-     * #property
-     */
     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]>;
@@ -117,17 +36,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             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]>;
-    /**
-     * #property
-     */
     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>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
@@ -137,6 +55,7 @@ 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>;
@@ -144,6 +63,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             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;
@@ -156,13 +76,19 @@ 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>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             * internal, a reference to a HTMLCanvas because we use a autorun to draw
+             * the canvas
+             */
             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>>;
     }> | null;
     readonly adapterConfig: any;
@@ -172,100 +98,66 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: 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;
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | 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";
-    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly renderDelay: number;
-    readonly TooltipComponent: React.FC<any>;
-    readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    setScrollTop(scrollTop: number): void;
+    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;
+    currStatsBpPerPx: number;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
     readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
-} & {
-    setMessage(message: string): void;
 } & {
     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;
+    setFeatureDensityStatsP(arg: any): void; /**
+     * #property
+     */
     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;
-    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;
-    reload(): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").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>;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
     loading: boolean;
-    drawn: boolean;
     chainData: ChainData | undefined;
+    lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
-    lastDrawnOffsetPx: number;
 } & {
     /**
      * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
      */
-    reload(): void;
+    setDrawSingletons(f: boolean): void;
     /**
      * #action
      */
-    setRef(ref: HTMLCanvasElement | null): void;
-    setColorScheme(s: {
-        type: string;
-    }): void;
+    setLastDrawnOffsetPx(n: number): void;
     /**
      * #action
      */
-    setChainData(args: ChainData): void;
+    setLastDrawnBpPerPx(n: number): void;
     /**
      * #action
      */
@@ -273,31 +165,46 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setDrawn(f: boolean): void;
+    reload(): void;
     /**
      * #action
+     * internal, a reference to a HTMLCanvas because we use a autorun to draw
+     * the canvas
      */
-    setFilterBy(filter: Filter): void;
+    setRef(ref: HTMLCanvasElement | null): void;
+    setColorScheme(s: {
+        type: string;
+    }): void;
     /**
      * #action
      */
-    setLastDrawnOffsetPx(n: number): void;
-} & {
+    setChainData(args: ChainData): void;
     /**
-     * #getter
+     * #action
      */
-    readonly ready: boolean;
-    readonly rendererTypeName: string;
+    setFilterBy(filter: Filter): void;
+} & {
+    readonly drawn: boolean;
+} & {
     renderProps(): any;
     /**
      * #method
      */
     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;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        icon?: undefined;
+        subMenu?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
         subMenu?: undefined;
     } | {
         label: string;
@@ -308,6 +215,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             label: string;
             onClick: () => void;
         }[];
+        type?: undefined;
+        checked?: undefined;
         onClick?: undefined;
     })[];
     /**
@@ -315,97 +224,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
-    }): Promise<JSX.Element | undefined>;
+    }): Promise<React.ReactNode>;
 } & {
     afterAttach(): void;
-}, {
-    type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    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>>;
-} & {
-    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>;
-        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>;
-        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;
-        filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            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;
-    userByteSizeLimit: number | undefined;
-} & import("mobx-state-tree")._NotCustomized>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type LinearReadCloudDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearReadCloudDisplayModel = Instance<LinearReadCloudDisplayStateModel>;
 export default stateModelFactory;