@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,13 +1,8 @@
-import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import { ColorBy, FilterBy } from '../shared/types';
-/**
- * #stateModel SharedLinearPileupDisplayMixin
- * #category display
- * extends `BaseLinearDisplay`
- */
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function SharedLinearPileupDisplayMixin(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>;
@@ -20,21 +15,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -52,21 +38,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -100,38 +80,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
-    /**
-     * #property
-     */
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    /**
-     * #property
-     */
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    /**
-     * #property
-     */
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -221,14 +178,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -255,68 +213,33 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
+    readonly hideSmallIndels: boolean | undefined;
 } & {
-    /**
-     * #action
-     */
     setTagsReady(flag: boolean): void;
-    /**
-     * #action
-     */
     setMaxHeight(n?: number): void;
-    /**
-     * #action
-     */
     setFeatureHeight(n?: number): void;
-    /**
-     * #action
-     */
     setNoSpacing(flag?: boolean): void;
-    /**
-     * #action
-     */
     setColorScheme(colorScheme: ColorBy): void;
-    /**
-     * #action
-     */
     updateColorTagMap(uniqueTag: string[]): void;
-    /**
-     * #action
-     */
     setFeatureUnderMouse(feat?: Feature): void;
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
-    /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
     copyFeatureToClipboard(feature: Feature): void;
-    /**
-     * #action
-     */
     setConfig(conf: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
-    /**
-     * #action
-     */
     setJexlFilters(filters: string[]): void;
+    setHideSmallIndels(arg: boolean): void;
 } & {
-    /**
-     * #getter
-     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -329,34 +252,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
-    /**
-     * #getter
-     */
     readonly maxHeight: any;
-    /**
-     * #getter
-     */
     readonly featureHeightSetting: any;
-    /**
-     * #getter
-     */
     readonly featureUnderMouse: Feature | undefined;
-    /**
-     * #getter
-     */
     renderReady(): boolean;
-    /**
-     * #getter
-     */
     readonly filters: SerializableFilterChain;
 } & {
-    /**
-     * #getter
-     */
     readonly rendererTypeName: string;
-    /**
-     * #method
-     */
     contextMenuItems(): ({
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -368,47 +270,38 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         icon: typeof ContentCopyIcon;
         onClick: () => void;
     })[];
-    /**
-     * #getter
-     */
     readonly DisplayBlurb: ({ model, }: {
         model: {
-            sortedBy?: {
-                pos: number;
-                refName: number;
-                type: string;
-                tag?: string;
-            };
+            sortedBy?: import("../shared/types").SortedBy;
         };
-    }) => import("react").JSX.Element | null;
-    /**
-     * #method
-     */
+    }) => import("react/jsx-runtime").JSX.Element | null;
     renderPropsPre(): any;
-    /**
-     * #method
-     */
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
-    /**
-     * #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;
+        priority: number;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        priority?: undefined;
+        type?: undefined;
+        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
 } & {
     afterAttach(): void;
-}, {
-    type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+}, import("mobx-state-tree").ModelCreationType<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>>;
@@ -420,21 +313,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -452,21 +336,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -499,12 +377,22 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: string;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    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>>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+}>>, {
     id: string;
+    type: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    heightPreConfig: number | undefined;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;