@apollo-annotation/jbrowse-plugin-apollo 0.3.10 → 0.3.12

package/dist/LinearApolloSixFrameDisplay/stateModel/mouseEvents.d.ts.map

@@ -0,0 +1 @@
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package/dist/LinearApolloSixFrameDisplay/stateModel/rendering.d.ts

@@ -0,0 +1,306 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { type Instance } from '@jbrowse/mobx-state-tree';
+import { type Theme } from '@mui/material';
+import type { ApolloSessionModel } from '../../session';
+export declare function renderingModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearApolloSixFrameDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    graphical: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    table: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showFeatureLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showStartCodons: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showStopCodons: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showCheckResults: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    zoomThreshold: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    filteredFeatureTypes: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    featuresMinMaxLimit: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+} & {
+    apolloRowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    detailsMinHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    detailsHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    lastRowTooltipBufferHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    isShown: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    filteredTranscripts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    statusMessage: string | undefined;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: () => void;
+        blockState?: Record<string, any>;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
+    readonly parentDisplay: any;
+    readonly effectiveRpcDriverName: any;
+} & {
+    renderProps(): any;
+    renderingProps(): {
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    };
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setStatusMessage(arg?: string): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    renderProps(): any;
+} & {
+    scrollTop: number;
+} & {
+    readonly lgv: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel;
+    readonly height: number;
+    readonly zoomThresholdSetting: number;
+} & {
+    readonly rendererTypeName: any;
+    readonly session: ApolloSessionModel;
+    readonly regions: {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
+    regionCannotBeRendered(): "Zoom in to see annotations" | undefined;
+} & {
+    readonly apolloInternetAccount: import("../../ApolloInternetAccount/model").ApolloInternetAccountModel | undefined;
+    readonly changeManager: import("../../ChangeManager").ChangeManager;
+    getAssemblyId(assemblyName: string): string;
+    readonly selectedFeature: import("@apollo-annotation/mst").AnnotationFeature | undefined;
+    readonly hoveredFeature: import("../../session").HoveredFeature | undefined;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    showGraphicalOnly(): void;
+    showTableOnly(): void;
+    showGraphicalAndTable(): void;
+    toggleShowFeatureLabels(): void;
+    toggleShowStartCodons(): void;
+    toggleShowStopCodons(): void;
+    toggleShowCheckResults(): void;
+    updateFilteredFeatureTypes(types: string[]): void;
+    setZoomThresholdSetting({ zoomThreshold }: {
+        zoomThreshold: number;
+    }): 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 | {
+        type: string;
+        label: string;
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        })[];
+    })[];
+} & {
+    setSelectedFeature(feature?: import("@apollo-annotation/mst").AnnotationFeature): void;
+    setHoveredFeature(hoveredFeature?: import("../../session").HoveredFeature): void;
+    showFeatureDetailsWidget(feature: import("@apollo-annotation/mst").AnnotationFeature, customWidgetNameAndId?: [string, string]): void;
+    afterAttach(): void;
+} & {
+    seenFeatures: import("mobx").ObservableMap<string, import("@apollo-annotation/mst").AnnotationFeature>;
+} & {
+    readonly featuresMinMax: (number[] | undefined)[];
+    getGlyph(_feature: import("@apollo-annotation/mst").AnnotationFeature): import("../glyphs/Glyph").Glyph;
+    featureLabelSpacer(elem: number): number;
+} & {
+    addSeenFeature(feature: import("@apollo-annotation/mst").AnnotationFeature): void;
+    deleteSeenFeature(featureId: string): void;
+} & {
+    readonly geneTrackRowNums: number[];
+} & {
+    readonly featureLayouts: Map<number, import("./layouts").LayoutRow[]>[];
+    getFeatureLayoutPosition(feature: import("@apollo-annotation/mst").AnnotationFeature): {
+        layoutIndex: number;
+        layoutRow: number;
+        featureRow: number;
+    } | undefined;
+} & {
+    readonly highestRow: number;
+} & {
+    afterAttach(): void;
+} & {
+    canvas: HTMLCanvasElement | null;
+    overlayCanvas: HTMLCanvasElement | null;
+    collaboratorCanvas: HTMLCanvasElement | null;
+    theme: Theme;
+} & {
+    readonly featuresHeight: number;
+} & {
+    toggleShown(): void;
+    setDetailsHeight(newHeight: number): void;
+    setCanvas(canvas: HTMLCanvasElement | null): void;
+    setOverlayCanvas(canvas: HTMLCanvasElement | null): void;
+    setCollaboratorCanvas(canvas: HTMLCanvasElement | null): void;
+    setTheme(theme: Theme): void;
+} & {
+    afterAttach(): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+export type LinearApolloSixFrameDisplayRenderingModel = ReturnType<typeof renderingModelFactory>;
+export interface LinearApolloSixFrameDisplayRendering extends Instance<LinearApolloSixFrameDisplayRenderingModel> {
+}
+//# sourceMappingURL=rendering.d.ts.map

package/dist/LinearApolloSixFrameDisplay/stateModel/rendering.d.ts.map

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package/dist/LinearApolloSixFrameDisplay/types.d.ts

@@ -0,0 +1,2 @@
+export type CanvasMouseEvent = React.MouseEvent<HTMLCanvasElement>;
+//# sourceMappingURL=types.d.ts.map

package/dist/LinearApolloSixFrameDisplay/types.d.ts.map

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package/dist/OntologyManager/OntologyStore/fulltext-stopwords.d.ts

@@ -0,0 +1,8 @@
+/** set of words that should be ignored by fulltext indexing */
+export declare const genericEnglishStopwords: Set<string>;
+/**
+ * The set of stopwords we use for fulltext indexing. Currently
+ * just generic English stopwords, but will likely be expanded over time.
+ */
+export declare const stopwords: Set<string>;
+//# sourceMappingURL=fulltext-stopwords.d.ts.map

package/dist/OntologyManager/OntologyStore/fulltext-stopwords.d.ts.map

@@ -0,0 +1 @@
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package/dist/OntologyManager/OntologyStore/fulltext.d.ts

@@ -0,0 +1,27 @@
+import type { TextIndexFieldDefinition } from '..';
+import type { OntologyDBNode } from './indexeddb-schema';
+import type OntologyStore from '.';
+import type { Transaction } from '.';
+/** special value of jsonPath that gets the IRI (that is, ID) of the node with the configured prefixes applied */
+export declare const PREFIXED_ID_PATH = "$PREFIXED_ID";
+/**
+ * recursively get the indexable words from an iterator
+ * of any objects
+ **/
+export declare function extractWords(strings: Iterable<string>): Generator<string, void, undefined>;
+export declare function extractStrings(things: Iterable<unknown>): Generator<string, void, undefined>;
+/** @returns generator of tuples of [jsonpath, word] */
+export declare function getWords(node: OntologyDBNode, jsonPaths: Iterable<string>, prefixes: Map<string, string>): Generator<[string, string], void, undefined>;
+export interface Match {
+    term: OntologyDBNode;
+    field: TextIndexFieldDefinition;
+    str: string;
+    score: number;
+}
+export declare function isMatch(thing: object): thing is Match;
+/**
+ *
+ **/
+export declare function textSearch(this: OntologyStore, text: string, tx?: Transaction<['nodes']>, signal?: AbortSignal): Promise<Match[]>;
+export declare function elaborateMatch(textIndexPaths: TextIndexFieldDefinition[], term: OntologyDBNode, queryWordIndexes: Set<number>, queryWords: string[], prefixes: Map<string, string>): Match[];
+//# sourceMappingURL=fulltext.d.ts.map

package/dist/OntologyManager/OntologyStore/fulltext.d.ts.map

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package/dist/OntologyManager/OntologyStore/index.d.ts

@@ -0,0 +1,93 @@
+import { type BlobLocation, type LocalPathLocation, type UriLocation } from '@jbrowse/core/util';
+import { type IDBPTransaction, type StoreNames } from 'idb/with-async-ittr';
+import { type OntologyClass, type OntologyProperty, type OntologyTerm } from '..';
+import { textSearch } from './fulltext';
+import { type OntologyDB } from './indexeddb-schema';
+import { isDatabaseCurrent, loadOboGraphJson, openDatabase } from './indexeddb-storage';
+export type SourceLocation = UriLocation | LocalPathLocation | BlobLocation;
+/** type alias for a Transaction on this particular DB schema */
+export type Transaction<TxStores extends ArrayLike<StoreNames<OntologyDB>> = ArrayLike<StoreNames<OntologyDB>>, Mode extends IDBTransactionMode = 'readonly'> = IDBPTransaction<OntologyDB, TxStores, Mode>;
+/** the format of the loading data source */
+type SourceType = 'obo-graph-json' | 'obo' | 'owl';
+export interface OntologyStoreOptions {
+    prefixes?: Map<string, string>;
+    textIndexing?: {
+        /** json paths of paths in the nodes to index as full text */
+        indexFields?: {
+            displayName: string;
+            jsonPath: string;
+        }[];
+    };
+    maxSearchResults?: number;
+    update?(message: string, progress: number): void;
+}
+export interface PropertiesOptions {
+    /** default true */
+    includeSubProperties: boolean;
+}
+/** query interface for a specific ontology */
+export default class OntologyStore {
+    ontologyName: string;
+    ontologyVersion: string;
+    sourceLocation: SourceLocation;
+    db: ReturnType<OntologyStore['prepareDatabase']>;
+    options: OntologyStoreOptions;
+    loadOboGraphJson: typeof loadOboGraphJson;
+    getTermsByFulltext: typeof textSearch;
+    openDatabase: typeof openDatabase;
+    isDatabaseCurrent: typeof isDatabaseCurrent;
+    get textIndexFields(): import("..").TextIndexFieldDefinition[];
+    get prefixes(): Map<string, string>;
+    readonly DEFAULT_MAX_SEARCH_RESULTS = 100;
+    constructor(name: string, version: string, source: SourceLocation, options?: OntologyStoreOptions);
+    /**
+     * check that the configuration of this ontology appears valid. Does not
+     * try to do any fetches, however.
+     */
+    validate(): Error[];
+    get sourceType(): SourceType | undefined;
+    /** base name of the IndexedDB database for this ontology */
+    get dbName(): string;
+    prepareDatabase(): Promise<import("idb/with-async-ittr").IDBPDatabase<OntologyDB>>;
+    termCount(tx?: Transaction<['nodes']>): Promise<number>;
+    private unique;
+    getTermsWithLabelOrSynonym(termLabelOrSynonym: string, options?: {
+        includeSubclasses?: boolean;
+    }, tx?: Transaction<['nodes', 'edges']>): Promise<OntologyTerm[]>;
+    /**
+     * Get the ontology term for the property with the given label,
+     * plus all the terms for the properties that are "subPropertyOf"
+     * that property.
+     *
+     * If there is more than one property with that label, treats it as
+     * equivalent and just returns all the properties and their subproperties.
+     *
+     * options.includeSubProperties default is true
+     */
+    getPropertiesByLabel(propertyLabel: string, options?: PropertiesOptions, tx?: Transaction<['nodes', 'edges']>): Promise<OntologyProperty[]>;
+    /** private helper for traversing the edges of the ontology graph. Does a breadth-first search of the graph */
+    private recurseEdges;
+    /**
+     * given an array of node IDs, augment it with all of their subclasses or
+     * superclasses, and return the augmented array
+     **/
+    private expandNodeSet;
+    /**
+     * given an iterator of node IDs, return a new iterator of those nodes plus all of their subclasses
+     */
+    expandSubclasses(startingNodeIds: Iterable<string>, subclassRelation?: string, tx?: Transaction<['edges']>): AsyncGenerator<string, void, unknown>;
+    /**
+     * given an iterator of node IDs, return a new iterator of those nodes plus all of their superclasses
+     */
+    expandSuperclasses(startingNodeIds: Iterable<string>, subclassRelation?: string, tx?: Transaction<['edges']>): AsyncGenerator<string, void, unknown>;
+    /**
+     * example: for the Sequence Ontology, store.getTermsThat('part_of', [geneTerm])
+     * would return all terms that are part_of, member_of, or integral_part_of a gene
+     */
+    getClassesThat(propertyLabel: string, targetTerms: OntologyClass[], tx?: Transaction<['nodes', 'edges']>): Promise<OntologyClass[]>;
+    getClassesWithoutPropertyLabeled(propertyLabel: string, options: PropertiesOptions, tx?: Transaction<['nodes', 'edges']>): Promise<OntologyClass[]>;
+    getAllClasses(tx?: Transaction<['nodes']>): Promise<OntologyClass[]>;
+    getAllTerms(tx?: Transaction<['nodes']>): Promise<OntologyTerm[]>;
+}
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/OntologyManager/OntologyStore/index.d.ts.map

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package/dist/OntologyManager/OntologyStore/indexeddb-schema.d.ts

@@ -0,0 +1,71 @@
+/** schema types used to strongly-type using the `idb` type system */
+import type { DBSchema } from 'idb/with-async-ittr';
+import type { Edge as OboGraphEdge, Meta as OboGraphMeta, Node as OboGraphNode } from './obo-graph-json-schema';
+import type { OntologyStoreOptions, SourceLocation } from '.';
+/** metadata about this IndexedDB ontology database */
+export interface Meta {
+    /** original OntologyManager record this was loaded from */
+    ontologyRecord: {
+        name: string;
+        version: string;
+        sourceLocation: SourceLocation;
+    };
+    storeOptions: OntologyStoreOptions;
+    /** graph metadata in OBO Graph metadata format */
+    graphMeta?: OboGraphMeta;
+    timestamp: string;
+    /** IndexedDB schemaVersion for this ontology */
+    schemaVersion: number;
+    /** time taken to load this data */
+    timings: {
+        /** milliseconds to fetch, parse, and load the ontology */
+        overall: number;
+        /** optional milliseconds to fetch the ontology source file over the network */
+        fetch?: number;
+        /** optional milliseconds to parse the ontology source file */
+        parse?: number;
+        /** optional milliseconds to load the ontology into IndexedDB */
+        load?: number;
+    };
+}
+export type OntologyDBNode = OboGraphNode & {
+    id: string;
+    type: 'CLASS' | 'INDIVIDUAL' | 'PROPERTY';
+    fullTextWords?: string[];
+};
+export declare function isOntologyDBNode(node: OboGraphNode): node is OntologyDBNode;
+export type OntologyDBEdge = OboGraphEdge & {
+    sub: string;
+    pred: string;
+    obj: string;
+};
+export declare function isOntologyDBEdge(edge: OboGraphEdge): edge is OntologyDBEdge;
+export declare function isDeprecated(thing: OntologyDBNode | OntologyDBEdge): boolean;
+/** schema types used to strongly-type using the `idb` type system */
+export interface OntologyDB extends DBSchema {
+    meta: {
+        key: string;
+        value: Meta;
+    };
+    nodes: {
+        key: string;
+        value: OntologyDBNode;
+        indexes: {
+            'by-label': string;
+            'by-type': string;
+            'by-synonym': string;
+            /** full-text index for fast searching by words */
+            'full-text-words': string;
+        };
+    };
+    edges: {
+        key: number;
+        value: OntologyDBEdge;
+        indexes: {
+            'by-subject': string;
+            'by-object': string;
+            'by-predicate': string;
+        };
+    };
+}
+//# sourceMappingURL=indexeddb-schema.d.ts.map

package/dist/OntologyManager/OntologyStore/indexeddb-schema.d.ts.map

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package/dist/OntologyManager/OntologyStore/indexeddb-storage.d.ts

@@ -0,0 +1,11 @@
+import { type IDBPDatabase } from 'idb/with-async-ittr';
+import { type OntologyDB } from './indexeddb-schema';
+import type OntologyStore from '.';
+export type Database = IDBPDatabase<OntologyDB>;
+/** open the IndexedDB and create the DB schema if necessary */
+export declare function openDatabase(this: OntologyStore, dbName: string): Promise<IDBPDatabase<OntologyDB>>;
+/** load a OBO Graph JSON file into a database */
+export declare function loadOboGraphJson(this: OntologyStore, db: Database): Promise<void>;
+export declare function getTextIndexFields(this: OntologyStore): import("..").TextIndexFieldDefinition[];
+export declare function isDatabaseCurrent(this: OntologyStore, db: Database): Promise<boolean>;
+//# sourceMappingURL=indexeddb-storage.d.ts.map

package/dist/OntologyManager/OntologyStore/indexeddb-storage.d.ts.map

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