@jbrowse/core 2.4.1 → 2.5.0

package/data_adapters/BaseAdapter.d.ts

@@ -1,138 +0,0 @@
-import { Observable } from 'rxjs';
-import { Feature } from '../util/simpleFeature';
-import { AnyConfigurationModel } from '../configuration';
-import { getSubAdapterType } from './dataAdapterCache';
-import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
-import BaseResult from '../TextSearch/BaseResults';
-import PluginManager from '../PluginManager';
-export interface BaseOptions {
-    signal?: AbortSignal;
-    bpPerPx?: number;
-    sessionId?: string;
-    statusCallback?: (message: string) => void;
-    headers?: Record<string, string>;
-    [key: string]: unknown;
-}
-export type SearchType = 'full' | 'prefix' | 'exact';
-export interface BaseArgs {
-    searchType?: SearchType;
-    queryString: string;
-    signal?: AbortSignal;
-    limit?: number;
-    pageNumber?: number;
-}
-export interface AnyAdapter {
-    new (config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager | undefined): AnyDataAdapter;
-}
-export type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | BaseSequenceAdapter;
-export interface SequenceAdapter extends BaseFeatureDataAdapter, RegionsAdapter {
-}
-export declare abstract class BaseAdapter {
-    config: AnyConfigurationModel;
-    getSubAdapter?: getSubAdapterType | undefined;
-    pluginManager?: PluginManager | undefined;
-    id: string;
-    static capabilities: string[];
-    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
-    getConf(arg: string | string[]): any;
-    /**
-     * Called to provide a hint that data tied to a certain region will not be
-     * needed for the foreseeable future and can be purged from caches, etc
-     * @param region - Region
-     */
-    abstract freeResources(region: Region): void;
-}
-export interface Stats {
-    featureDensity?: number;
-    fetchSizeLimit?: number;
-    bytes?: number;
-}
-/**
- * Base class for feature adapters to extend. Defines some methods that
- * subclasses must implement.
- */
-export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
-    /**
-     * Get all reference sequence names used in the data source
-     *
-     * NOTE: If an adapter is unable to determine the reference sequence names,
-     * the array will be empty
-     * @param opts - Feature adapter options
-     */
-    abstract getRefNames(opts?: BaseOptions): Promise<string[]>;
-    /**
-     * Get features from the data source that overlap a region
-     * @param region - Region
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the region
-     */
-    abstract getFeatures(region: Region, opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Return "header info" that is fetched from the data file, or other info
-     * that would not simply be in the config of the file. The return value can
-     * be `{tag:string, data: any}[]` e.g. list of tags with their values which
-     * is how VCF,BAM,CRAM return values for getInfo or it can be a nested JSON
-     * object
-     */
-    getHeader(_opts?: BaseOptions): Promise<unknown>;
-    /**
-     * Return info that is primarily used for interpreting the data that is there,
-     * primarily in reference to being used for augmenting feature details panels
-     */
-    getMetadata(_opts?: BaseOptions): Promise<unknown>;
-    /**
-     * Checks if the store has data for the given assembly and reference
-     * sequence, and then gets the features in the region if it does.
-     */
-    getFeaturesInRegion(region: Region, opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Checks if the store has data for the given assembly and reference
-     * sequence, and then gets the features in the region if it does.
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters
-     * that are frequently called on multiple regions simultaneously may
-     * want to implement a more efficient custom version of this method.
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Check if the store has data for the given reference name.
-     * @param refName - Name of the reference sequence
-     * @returns Whether data source has data for the given reference name
-     */
-    hasDataForRefName(refName: string, opts?: BaseOptions): Promise<boolean>;
-    getRegionStats(region: Region, opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
-    getMultiRegionStats(regions?: Region[], opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<Stats>;
-}
-export interface RegionsAdapter extends BaseAdapter {
-    getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
-}
-export declare abstract class BaseSequenceAdapter extends BaseFeatureDataAdapter implements RegionsAdapter {
-    estimateRegionsStats(): Promise<{
-        featureDensity: number;
-    }>;
-    abstract getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
-}
-export declare function isSequenceAdapter(thing: AnyDataAdapter): thing is BaseSequenceAdapter;
-export declare function isRegionsAdapter(thing: AnyDataAdapter): thing is RegionsAdapter;
-export declare function isFeatureAdapter(thing: AnyDataAdapter): thing is BaseFeatureDataAdapter;
-export interface Alias {
-    refName: string;
-    aliases: string[];
-}
-export interface BaseRefNameAliasAdapter extends BaseAdapter {
-    getRefNameAliases(opts: BaseOptions): Promise<Alias[]>;
-}
-export declare function isRefNameAliasAdapter(thing: object): thing is BaseRefNameAliasAdapter;
-export interface BaseTextSearchAdapter extends BaseAdapter {
-    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
-}
-export declare function isTextSearchAdapter(thing: AnyDataAdapter): thing is BaseTextSearchAdapter;