@jbrowse/core 3.7.0 → 4.0.1

package/util/types/mst.d.ts

@@ -1,107 +0,0 @@
-export declare const ElementId: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-export declare const NoAssemblyRegion: 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]>;
-}, {
-    setRefName(newRefName: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare const 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>;
-export declare const LocalPathLocation: import("mobx-state-tree").IModelType<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare const BlobLocation: import("mobx-state-tree").IModelType<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare const UriLocationRaw: import("mobx-state-tree").IModelType<{
-    locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-    uri: import("mobx-state-tree").ISimpleType<string>;
-    baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare const UriLocation: import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").IModelType<{
-    locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-    uri: import("mobx-state-tree").ISimpleType<string>;
-    baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, import("mobx-state-tree")._NotCustomized, {
-    locationType: "UriLocation";
-    uri: string;
-    internetAccountId: string | undefined;
-    internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }> | undefined;
-}>;
-export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-    uri: import("mobx-state-tree").ISimpleType<string>;
-    baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}>>, {
-    locationType: "UriLocation";
-    uri: string;
-    internetAccountId: string | undefined;
-    internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }> | undefined;
-} | import("mobx-state-tree").ModelSnapshotType<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}> | import("mobx-state-tree").ModelSnapshotType<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}>, import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}, {}> | import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}, {}> | ({
-    locationType: "UriLocation";
-    uri: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-    uri: import("mobx-state-tree").ISimpleType<string>;
-    baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-        authInfo: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/util/types/mst.js

@@ -1,72 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.FileLocation = exports.UriLocation = exports.UriLocationRaw = exports.BlobLocation = exports.LocalPathLocation = exports.Region = exports.NoAssemblyRegion = exports.ElementId = void 0;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const nanoid_1 = require("../nanoid");
-exports.ElementId = mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, () => (0, nanoid_1.nanoid)());
-exports.NoAssemblyRegion = mobx_state_tree_1.types
-    .model('NoAssemblyRegion', {
-    refName: mobx_state_tree_1.types.string,
-    start: mobx_state_tree_1.types.number,
-    end: mobx_state_tree_1.types.number,
-    reversed: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, false),
-})
-    .actions(self => ({
-    setRefName(newRefName) {
-        self.refName = newRefName;
-    },
-}));
-exports.Region = mobx_state_tree_1.types.compose('Region', exports.NoAssemblyRegion, mobx_state_tree_1.types.model({
-    assemblyName: mobx_state_tree_1.types.string,
-}));
-exports.LocalPathLocation = mobx_state_tree_1.types.model('LocalPathLocation', {
-    locationType: mobx_state_tree_1.types.literal('LocalPathLocation'),
-    localPath: mobx_state_tree_1.types.string,
-});
-exports.BlobLocation = mobx_state_tree_1.types.model('BlobLocation', {
-    locationType: mobx_state_tree_1.types.literal('BlobLocation'),
-    name: mobx_state_tree_1.types.string,
-    blobId: mobx_state_tree_1.types.string,
-});
-exports.UriLocationRaw = mobx_state_tree_1.types.model('UriLocation', {
-    locationType: mobx_state_tree_1.types.literal('UriLocation'),
-    uri: mobx_state_tree_1.types.string,
-    baseUri: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    internetAccountId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    internetAccountPreAuthorization: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model('InternetAccountPreAuthorization', {
-        internetAccountType: mobx_state_tree_1.types.string,
-        authInfo: mobx_state_tree_1.types.frozen(),
-    })),
-});
-exports.UriLocation = mobx_state_tree_1.types.snapshotProcessor(exports.UriLocationRaw, {
-    postProcessor: snap => {
-        const { baseUri, ...rest } = snap;
-        if (!baseUri) {
-            return rest;
-        }
-        return snap;
-    },
-});
-exports.FileLocation = mobx_state_tree_1.types.snapshotProcessor(mobx_state_tree_1.types.union(exports.LocalPathLocation, exports.UriLocation, exports.BlobLocation), {
-    preProcessor(snap) {
-        if (!snap) {
-            return undefined;
-        }
-        const { locationType, ...rest } = snap;
-        if (!locationType) {
-            const { uri, localPath, blob } = rest;
-            let locationType = '';
-            if (uri !== undefined) {
-                locationType = 'UriLocation';
-            }
-            else if (localPath !== undefined) {
-                locationType = 'LocalPathLocation';
-            }
-            else if (blob !== undefined) {
-                locationType = 'BlobLocation';
-            }
-            return { ...rest, locationType };
-        }
-        return snap;
-    },
-});

package/util/types/util.d.ts

@@ -1,6 +0,0 @@
-import type React from 'react';
-import type PluginManager from '../../PluginManager';
-export type InstanceTypeRestrictive<CONSTRUCTOR extends new (...args: any[]) => any> = CONSTRUCTOR extends new (...args: any[]) => infer CLASS ? CLASS : never;
-export type ClassReturnedBy<FACT extends (pm: PluginManager) => any> = InstanceTypeRestrictive<ReturnType<FACT>>;
-export type AnyReactComponentType = React.ComponentType<any>;
-export type TypeTestedByPredicate<PREDICATE extends (thing: any) => boolean> = PREDICATE extends (thing: any) => thing is infer TYPE ? TYPE : never;

package/util/types/util.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/util/useFeatureSequence.d.ts

@@ -1,19 +0,0 @@
-import type { AbstractSessionModel, Feature } from '.';
-export declare function useFeatureSequence({ session, feature, upDownBp, forceLoad, assemblyName, shouldFetch, }: {
-    assemblyName: string;
-    session?: AbstractSessionModel;
-    feature: Feature;
-    upDownBp: number;
-    forceLoad: boolean;
-    shouldFetch?: boolean;
-}): {
-    sequence: {
-        seq: string;
-        upstream: string;
-        downstream: string;
-    } | {
-        error: string;
-    } | undefined;
-    loading: boolean;
-    error: unknown;
-};

package/util/useFeatureSequence.js

@@ -1,90 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.useFeatureSequence = useFeatureSequence;
-const react_1 = require("react");
-const fetchSeq_1 = require("./fetchSeq");
-const BPLIMIT = 20000000;
-function useFeatureSequence({ session, feature, upDownBp, forceLoad, assemblyName, shouldFetch = true, }) {
-    const [sequence, setSequence] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const key = (0, react_1.useMemo)(() => {
-        if (!session || !shouldFetch) {
-            return null;
-        }
-        const start = feature.get('start');
-        const end = feature.get('end');
-        const refName = feature.get('refName');
-        return {
-            start,
-            end,
-            refName,
-            assemblyName,
-            upDownBp,
-            forceLoad,
-            sessionId: session.id || 'default',
-        };
-    }, [session, feature, assemblyName, upDownBp, forceLoad, shouldFetch]);
-    (0, react_1.useEffect)(() => {
-        if (!key) {
-            setSequence(undefined);
-            setError(undefined);
-            return;
-        }
-        ;
-        (async () => {
-            try {
-                setLoading(true);
-                setError(undefined);
-                const { start, end, refName, assemblyName, upDownBp, forceLoad } = key;
-                if (!forceLoad && end - start > BPLIMIT) {
-                    setSequence({
-                        error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
-                    });
-                    return;
-                }
-                const b = start - upDownBp;
-                const e = end + upDownBp;
-                const [seq, upstream, downstream] = await Promise.all([
-                    (0, fetchSeq_1.fetchSeq)({
-                        start,
-                        end,
-                        refName,
-                        assemblyName,
-                        session: session,
-                    }),
-                    (0, fetchSeq_1.fetchSeq)({
-                        start: Math.max(0, b),
-                        end: start,
-                        refName,
-                        assemblyName,
-                        session: session,
-                    }),
-                    (0, fetchSeq_1.fetchSeq)({
-                        start: end,
-                        end: e,
-                        refName,
-                        assemblyName,
-                        session: session,
-                    }),
-                ]);
-                setSequence({
-                    seq,
-                    upstream,
-                    downstream,
-                });
-            }
-            catch (err) {
-                setError(err);
-            }
-            finally {
-                setLoading(false);
-            }
-        })();
-    }, [key, session]);
-    return {
-        sequence,
-        loading,
-        error,
-    };
-}

package/util/useMeasure.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = useMeasure;
-const react_1 = require("react");
-function useMeasure() {
-    const ref = (0, react_1.useRef)(null);
-    const [dims, setDims] = (0, react_1.useState)({
-        width: undefined,
-        height: undefined,
-    });
-    (0, react_1.useEffect)(() => {
-        if (!ref.current) {
-            return;
-        }
-        const RS = typeof window !== 'undefined' && 'ResizeObserver' in window
-            ? window.ResizeObserver
-            : undefined;
-        if (!RS) {
-            return;
-        }
-        const observer = new RS(entries => {
-            setDims({
-                width: entries[0].contentRect.width,
-                height: entries[0].contentRect.height,
-            });
-        });
-        observer.observe(ref.current);
-        return () => {
-            observer.disconnect();
-        };
-    }, []);
-    return [ref, dims];
-}

package/util/when.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.when = void 0;
-var mobx_1 = require("mobx");
-Object.defineProperty(exports, "when", { enumerable: true, get: function () { return mobx_1.when; } });