@jbrowse/plugin-alignments 2.6.2 → 2.6.3

package/esm/LinearPileupDisplay/model.d.ts

@@ -1,8 +1,6 @@
 /// <reference types="react" />
 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';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export interface Filter {
     flagInclude: number;
     flagExclude: number;
@@ -43,10 +41,15 @@ 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>;
     }, {
+        /**
+         * #stateModel LinearPileupDisplay
+         * #category display
+         * extends `BaseLinearDisplay`
+         */
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -59,14 +62,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
-         * #property
-         */
+        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, Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -89,7 +90,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         height: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #stateModel LinearPileupDisplay
+             * #category display
+             * extends `BaseLinearDisplay`
+             */
         };
         mouseover: {
             type: string;
@@ -99,21 +104,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     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>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        pos: import("mobx-state-tree").ISimpleType<number>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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>>;
@@ -128,6 +123,18 @@ 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]>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        pos: import("mobx-state-tree").ISimpleType<number>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -174,9 +181,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any; /**
-     * #property
-     */
+    readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
@@ -223,7 +228,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
     featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -233,20 +238,22 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined; /**
-     * #action
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
+     * #getter
      */
+    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;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+     * #method
+     */
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -258,75 +265,97 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    modificationTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: Feature | undefined;
-    currSortBpPerPx: number;
-    modificationsReady: boolean;
-    sortReady: boolean;
+    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
-    /**
-     * #action
-     */
-    setModificationsReady(flag: boolean): void;
-    /**
-     * #action
-     */
     setTagsReady(flag: boolean): void;
-    /**
-     * #action
-     */
-    setSortReady(flag: boolean): void;
-    /**
-     * #action
-     */
-    setCurrSortBpPerPx(n: number): void;
-    /**
-     * #action
-     */
     setMaxHeight(n: number): void;
-    /**
-     * #action
-     */
-    setFeatureHeight(n?: number): void;
-    /**
-     * #action
-     */
-    setNoSpacing(flag?: boolean): void;
-    /**
-     * #action
-     */
+    setFeatureHeight(n?: number | undefined): void;
+    setNoSpacing(flag?: boolean | undefined): void;
     setColorScheme(colorScheme: {
         type: string;
-        tag?: string;
+        tag?: string | undefined;
+        extra?: import("../shared/color").ExtraColorBy | undefined;
     }): void;
+    updateColorTagMap(uniqueTag: string[]): void;
+    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
+    setConfig(conf: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
+    setFilterBy(filter: import("./SharedLinearPileupDisplayMixin").Filter): void;
+} & {
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    readonly maxHeight: any;
+    readonly featureHeightSetting: any;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    renderReady(): boolean;
+} & {
+    readonly rendererTypeName: string;
+    contextMenuItems(): ({
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    } | {
+        label: string;
+        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
+        onClick: () => void;
+    })[];
+    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    renderPropsPre(): any;
+    colorSchemeSubMenuItems(): {
+        label: string;
+        onClick: () => void;
+    }[];
+    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;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    })[];
+} & {
+    renderProps(): any;
+} & {
+    afterAttach(): void;
+} & {
+    sortReady: boolean;
+    currSortBpPerPx: number;
+    modificationTagMap: import("mobx").ObservableMap<string, string>;
+    modificationsReady: boolean;
+} & {
     /**
      * #action
      */
-    updateModificationColorMap(uniqueModifications: string[]): void;
+    setCurrSortBpPerPx(n: number): void;
     /**
      * #action
      */
-    updateColorTagMap(uniqueTag: string[]): void;
+    updateModificationColorMap(uniqueModifications: string[]): void;
     /**
      * #action
      */
-    setFeatureUnderMouse(feat?: Feature): void;
+    setModificationsReady(flag: boolean): void;
     /**
      * #action
      */
-    selectFeature(feature: Feature): void;
+    setSortReady(flag: boolean): void;
     /**
      * #action
      */
     clearSelected(): void;
-    /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
-    copyFeatureToClipboard(feature: Feature): void;
     /**
      * #action
      */
@@ -335,15 +364,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     toggleMismatchAlpha(): void;
-    /**
-     * #action
-     */
-    setConfig(conf: AnyConfigurationModel): void;
     /**
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
-    setFilterBy(filter: Filter): void;
 } & {
     /**
      * #action
@@ -359,14 +383,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
-    /**
-     * #getter
-     */
-    readonly maxHeight: any;
-    /**
-     * #getter
-     */
-    readonly featureHeightSetting: any;
     /**
      * #getter
      */
@@ -374,34 +390,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #getter
      */
-    readonly featureUnderMouse: Feature | undefined;
-    /**
-     * #getter
-     */
-    readonly renderReady: boolean;
+    renderReady(): boolean;
 } & {
-    /**
-     * #getter
-     */
-    readonly rendererTypeName: string;
-    /**
-     * #method
-     */
-    contextMenuItems(): ({
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof ContentCopyIcon;
-        onClick: () => void;
-    })[];
-    /**
-     * #getter
-     */
-    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
     /**
      * #method
      */
@@ -438,27 +428,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         onClick?: undefined;
     } | {
         label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
         subMenu: {
             label: string;
             onClick: () => void;
         }[];
+        icon?: undefined;
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
         disabled?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
     } | {
         label: string;
         type: string;
@@ -470,98 +448,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     })[];
 } & {
     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>>;
-} & {
-    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<{
-            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, 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; /**
-         * #property
-         */
-        setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            features: Map<string, 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>>;
-    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 LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
 export default stateModelFactory;