@jbrowse/app-core 4.3.0 → 5.0.0-beta.2

package/esm/JbApi/jbApi.d.ts

@@ -0,0 +1,325 @@
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
+import { getFeatureAdapterOrThrow } from '@jbrowse/core/data_adapters/getFeatureAdapter';
+import { getRpcSessionId, parseLocString, renameRegionsIfNeeded } from '@jbrowse/core/util';
+import { createStopToken, stopStopToken } from '@jbrowse/core/util/stopToken';
+import * as mst from '@jbrowse/mobx-state-tree';
+import * as mobx from 'mobx';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AbstractSessionModel } from '@jbrowse/core/util/types';
+import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
+/**
+ * What jb.getFeatures may pull before it refuses. An explicit request wins so
+ * an agent can mean it; otherwise the adapter's own declared limit, so this
+ * does not disagree with the size the track's display already refuses to
+ * render; otherwise the default.
+ */
+export declare function agentByteLimit(declaredFetchSizeLimit: unknown, requested?: number): number;
+interface DisplaySelf {
+    type: string;
+    configuration: AnyConfigurationModel;
+    displayPhase?: string;
+    regionTooLargeReason?: string;
+    height?: number;
+    error?: unknown;
+}
+interface TrackSelf extends IStateTreeNode {
+    type: string;
+    configuration: AnyConfigurationModel & {
+        trackId: string;
+    };
+    displays?: (Record<string, unknown> & DisplaySelf)[];
+}
+export declare function sessionOf(pluginManager: PluginManager | undefined): AbstractSessionModel | undefined;
+export declare function safeJson(value: unknown): string;
+export declare function undeliveredNotifications(session: AbstractSessionModel): {
+    level: string;
+    message: string;
+}[];
+export declare function waitReady(timeoutMs: number, session?: AbstractSessionModel, root?: ParentNode): Promise<{
+    settled: boolean;
+    notifications?: {
+        level: string;
+        message: string;
+    }[] | undefined;
+    notReady?: (({
+        trackId: string;
+    } & Record<"error", unknown>) | ({
+        trackId: string;
+    } & Record<"phase", unknown>))[] | undefined;
+    offscreen?: {
+        pageHeight: number;
+        windowHeight: number;
+        views: {
+            viewId: string;
+            top: number;
+            bottom: number;
+        }[];
+        note: string;
+    } | undefined;
+} | {
+    settled: boolean;
+    note: string;
+    notifications?: {
+        level: string;
+        message: string;
+    }[] | undefined;
+    notReady?: (({
+        trackId: string;
+    } & Record<"error", unknown>) | ({
+        trackId: string;
+    } & Record<"phase", unknown>))[] | undefined;
+    offscreen?: {
+        pageHeight: number;
+        windowHeight: number;
+        views: {
+            viewId: string;
+            top: number;
+            bottom: number;
+        }[];
+        note: string;
+    } | undefined;
+}>;
+interface JbRegion {
+    refName: string;
+    start: number;
+    end: number;
+    assemblyName: string;
+}
+interface SlotDescription {
+    type: string;
+    description?: string;
+    defaultValue: unknown;
+}
+declare function describeSlots(conf: AnyConfigurationModel): Record<string, SlotDescription>;
+export declare function ensureReExports(): Promise<void>;
+export declare function createJbApi(pluginManager: PluginManager): {
+    readonly session: AbstractSessionModel;
+    readonly rootModel: import("@jbrowse/core/util").AbstractRootModel | undefined;
+    require: (lib: string | ((...args: any) => any) | {
+        default: (...args: any) => any;
+    }) => any;
+    ensureRequire: typeof ensureReExports;
+    mst: typeof mst;
+    mobx: typeof mobx;
+    readConfObject: typeof readConfObject;
+    getConf: typeof getConf;
+    describeSlots: typeof describeSlots;
+    parseLocString: typeof parseLocString;
+    getFeatureAdapterOrThrow: typeof getFeatureAdapterOrThrow;
+    getRpcSessionId: typeof getRpcSessionId;
+    renameRegionsIfNeeded: typeof renameRegionsIfNeeded;
+    createStopToken: typeof createStopToken;
+    stopStopToken: typeof stopStopToken;
+    waitReady: (timeoutMs: number) => Promise<{
+        settled: boolean;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+    } | {
+        settled: boolean;
+        note: string;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+    }>;
+    sessionSummary: () => {
+        name: string;
+        assemblyNames: string[];
+        views: Record<string, unknown>[];
+    };
+    inspect: (path?: string, maxInspectBytes?: number) => {
+        path: string;
+        modelType?: string | undefined;
+        bytes: number;
+        getters?: string[] | undefined;
+        actions?: string[] | undefined;
+        value: unknown;
+    } | {
+        path: string;
+        modelType?: string | undefined;
+        bytes: number;
+        getters?: string[] | undefined;
+        actions?: string[] | undefined;
+        note: string;
+        items: string[];
+    } | {
+        path: string;
+        modelType?: string | undefined;
+        bytes: number;
+        getters?: string[] | undefined;
+        actions?: string[] | undefined;
+        note: string;
+        keys: {
+            [k: string]: string;
+        };
+    };
+    listTracks: (search?: string, limit?: number) => {
+        total: number;
+        note?: string | undefined;
+        tracks: {
+            trackId: any;
+            name: string;
+            type: any;
+            adapterType?: any;
+            assemblyNames: string[];
+        }[];
+    };
+    trackModel: (trackId: string) => TrackSelf | undefined;
+    visibleRegions: (viewId?: string) => Promise<JbRegion[]>;
+    loadSessionSpec: (spec: Record<string, unknown>, settleMs?: number) => Promise<{
+        settled: boolean;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+        session?: {
+            name: string;
+            assemblyNames: string[];
+            views: Record<string, unknown>[];
+        } | undefined;
+    } | {
+        settled: boolean;
+        note: string;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+        session?: {
+            name: string;
+            assemblyNames: string[];
+            views: Record<string, unknown>[];
+        } | undefined;
+    }>;
+    addTrack: (opts: Record<string, unknown>) => Promise<{
+        trackId: string;
+        trackType: string;
+        adapterType: string;
+        assembly: string;
+    } | {
+        settled: boolean;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+        trackId: string;
+        trackType: string;
+        adapterType: string;
+        assembly: string;
+        shownInView: string;
+    } | {
+        settled: boolean;
+        note: string;
+        notifications?: {
+            level: string;
+            message: string;
+        }[] | undefined;
+        notReady?: (({
+            trackId: string;
+        } & Record<"error", unknown>) | ({
+            trackId: string;
+        } & Record<"phase", unknown>))[] | undefined;
+        offscreen?: {
+            pageHeight: number;
+            windowHeight: number;
+            views: {
+                viewId: string;
+                top: number;
+                bottom: number;
+            }[];
+            note: string;
+        } | undefined;
+        trackId: string;
+        trackType: string;
+        adapterType: string;
+        assembly: string;
+        shownInView: string;
+    }>;
+    getFeatures: (args: string | {
+        trackId: string;
+        loc?: string;
+        assembly?: string;
+        regions?: JbRegion[];
+        viewId?: string;
+        byteLimit?: number;
+    }, positionalLoc?: string) => Promise<import("@jbrowse/core/util").Feature[]>;
+};
+export type JbApi = ReturnType<typeof createJbApi>;
+export {};