@jbrowse/plugin-alignments 1.7.0 → 1.7.1

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,10 +1,10 @@
-/// <reference types="react" />
-declare type Coord = [number, number];
-declare const SNPCoverageTooltip: (props: {
-    model: any;
-    height: number;
-    offsetMouseCoord: Coord;
-    clientMouseCoord: Coord;
-    clientRect?: DOMRect;
-}) => JSX.Element | null;
-export default SNPCoverageTooltip;
+/// <reference types="react" />
+declare type Coord = [number, number];
+declare const SNPCoverageTooltip: (props: {
+    model: any;
+    height: number;
+    offsetMouseCoord: Coord;
+    clientMouseCoord: Coord;
+    clientRect?: DOMRect;
+}) => JSX.Element | null;
+export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/index.d.ts

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

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

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

@@ -1,96 +1,346 @@
-/// <reference types="react" />
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    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: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, 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: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, 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>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
-    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    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>>;
-        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>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    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>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, never, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
-export default stateModelFactory;
+/// <reference types="react" />
+import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    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: import("react").ReactElement<any, string | import("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: import("react").ReactElement<any, string | import("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>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
+    drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    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>>;
+        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>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    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>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: import("mobx-state-tree").ModelInstanceTypeProps<{
+            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>>;
+        }> & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: import("mobx-state-tree").ModelInstanceTypeProps<{
+            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>>;
+        }> & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: any;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    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): any;
+    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(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): 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 | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    statsReady: boolean;
+    message: string | undefined;
+    stats: {
+        scoreMin: number;
+        scoreMax: number;
+    };
+    statsFetchInProgress: AbortController | undefined;
+} & {
+    updateStats({ scoreMin, scoreMax, }: {
+        scoreMin: number;
+        scoreMax: number;
+    }): void;
+    setColor(color: string): void;
+    setPosColor(color: string): void;
+    setNegColor(color: string): void;
+    setLoading(aborter: AbortController): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    setResolution(res: number): void;
+    setFill(fill: boolean): void;
+    toggleLogScale(): void;
+    setScaleType(scale?: string | undefined): void;
+    setSummaryScoreMode(val: string): void;
+    setAutoscale(val: string): void;
+    setMaxScore(val?: number | undefined): void;
+    setRendererType(val: string): void;
+    setMinScore(val?: number | undefined): void;
+    toggleCrossHatches(): void;
+    setCrossHatches(cross: boolean): void;
+} & {
+    readonly TooltipComponent: import("react").FC<{}>;
+    readonly adapterTypeName: any;
+    readonly rendererTypeName: string;
+    readonly filters: undefined;
+    readonly scaleType: any;
+    readonly maxScore: any;
+    readonly minScore: any;
+} & {
+    readonly rendererConfig: any;
+} & {
+    readonly filled: any;
+    readonly summaryScoreModeSetting: any;
+    readonly domain: number[];
+    readonly needsScalebar: boolean;
+    readonly scaleOpts: {
+        domain: number[];
+        stats: {
+            scoreMin: number;
+            scoreMax: number;
+        };
+        autoscaleType: any;
+        scaleType: any;
+        inverted: any;
+    };
+    readonly canHaveFill: boolean;
+    readonly autoscaleType: any;
+    readonly displayCrossHatchesSetting: any;
+} & {
+    readonly ticks: any;
+} & {
+    renderProps(): any;
+    readonly adapterCapabilities: string[];
+    readonly hasResolution: boolean;
+    readonly hasGlobalStats: boolean;
+} & {
+    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 | {
+        type: string;
+        label: string;
+        checked: any;
+        onClick: () => void;
+    })[];
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    modificationTagMap: import("mobx").ObservableMap<any, any>;
+} & {
+    setConfig(configuration: AnyConfigurationModel): void;
+    setFilterBy(filter: {
+        flagInclude: number;
+        flagExclude: number;
+        readName?: string;
+        tagFilter?: {
+            tag: string;
+            value: string;
+        };
+    }): void;
+    setColorBy(colorBy?: {
+        type: string;
+        tag?: string | undefined;
+    } | undefined): void;
+    updateModificationColorMap(uniqueModifications: string[]): void;
+} & {
+    readonly rendererConfig: any;
+    readonly drawArcsSetting: any;
+    readonly drawInterbaseCountsSetting: any;
+    readonly drawIndicatorsSetting: any;
+    readonly modificationsReady: boolean;
+    renderProps(): any;
+} & {
+    toggleDrawIndicators(): void;
+    toggleDrawInterbaseCounts(): void;
+    toggleDrawArcs(): void;
+    afterAttach(): void;
+} & {
+    readonly TooltipComponent: (props: {
+        model: any;
+        height: number;
+        offsetMouseCoord: [number, number];
+        clientMouseCoord: [number, number];
+        clientRect?: DOMRect | undefined;
+    }) => JSX.Element | null;
+    readonly adapterConfig: {
+        type: string;
+        subadapter: any;
+    };
+    readonly rendererTypeName: string | undefined;
+    readonly needsScalebar: boolean;
+    contextMenuItems(): never[];
+    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: any;
+        onClick: () => void;
+    })[];
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export declare type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
+export default stateModelFactory;

package/dist/NestedFrequencyTable.d.ts

@@ -1,14 +1,14 @@
-export default class NestedFrequencyTable {
-    categories: {
-        [key: string]: any;
-    };
-    constructor(initialData?: {});
-    total(): number;
-    decrement(slotName: string, amount: number): any;
-    increment(slotName: string, amount: number): any;
-    get(slotName: string): any;
-    getNested(path: string | string[]): any;
-    toString(): string;
-    valueOf(): number;
-    forEach(func: Function, ctx: any): void;
-}
+export default class NestedFrequencyTable {
+    categories: {
+        [key: string]: any;
+    };
+    constructor(initialData?: {});
+    total(): number;
+    decrement(slotName: string, amount: number): any;
+    increment(slotName: string, amount: number): any;
+    get(slotName: string): any;
+    getNested(path: string | string[]): any;
+    toString(): string;
+    valueOf(): number;
+    forEach(func: Function, ctx: any): void;
+}

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,34 +1,34 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-export declare class PileupGetGlobalValueForTag extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
-export declare class PileupGetVisibleModifications extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util/types';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+export declare class PileupGetGlobalValueForTag extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}
+export declare class PileupGetVisibleModifications extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}

package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,29 +1,29 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
-export interface PileupLayoutSessionProps {
-    config: AnyConfigurationModel;
-    bpPerPx: number;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: unknown;
-}
-declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-interface CachedPileupLayout {
-    layout: MyMultiLayout;
-    config: AnyConfigurationModel;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: boolean;
-}
-export declare class PileupLayoutSession extends LayoutSession {
-    sortedBy: unknown;
-    showSoftClip: boolean;
-    constructor(args: PileupLayoutSessionProps);
-    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
-    cachedLayout: CachedPileupLayout | undefined;
-    get layout(): MyMultiLayout;
-}
-export {};
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+export interface PileupLayoutSessionProps {
+    config: AnyConfigurationModel;
+    bpPerPx: number;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: unknown;
+}
+declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+interface CachedPileupLayout {
+    layout: MyMultiLayout;
+    config: AnyConfigurationModel;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: boolean;
+}
+export declare class PileupLayoutSession extends LayoutSession {
+    sortedBy: unknown;
+    showSoftClip: boolean;
+    constructor(args: PileupLayoutSessionProps);
+    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
+    cachedLayout: CachedPileupLayout | undefined;
+    get layout(): MyMultiLayout;
+}
+export {};