@jbrowse/core 3.7.0 → 4.0.1

package/esm/util/types/mst.d.ts

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

package/esm/util/types/mst.js

@@ -0,0 +1,68 @@
+import { types } from '@jbrowse/mobx-state-tree';
+export const NoAssemblyRegion = types
+    .model('NoAssemblyRegion', {
+    refName: types.string,
+    start: types.number,
+    end: types.number,
+    reversed: types.optional(types.boolean, false),
+})
+    .actions(self => ({
+    setRefName(newRefName) {
+        self.refName = newRefName;
+    },
+}));
+export const Region = types.compose('Region', NoAssemblyRegion, types.model({
+    assemblyName: types.string,
+}));
+export const LocalPathLocation = types.model('LocalPathLocation', {
+    locationType: types.literal('LocalPathLocation'),
+    localPath: types.string,
+});
+export const BlobLocation = types.model('BlobLocation', {
+    locationType: types.literal('BlobLocation'),
+    name: types.string,
+    blobId: types.string,
+});
+export const UriLocationRaw = types.model('UriLocation', {
+    locationType: types.literal('UriLocation'),
+    uri: types.string,
+    baseUri: types.maybe(types.string),
+    internetAccountId: types.maybe(types.string),
+    internetAccountPreAuthorization: types.maybe(types.model('InternetAccountPreAuthorization', {
+        internetAccountType: types.string,
+        authInfo: types.frozen(),
+    })),
+});
+export const UriLocation = types.snapshotProcessor(UriLocationRaw, {
+    postProcessor: snap => {
+        const { baseUri, ...rest } = snap;
+        if (!baseUri) {
+            return rest;
+        }
+        return snap;
+    },
+});
+export const FileLocation = types.snapshotProcessor(types.union(LocalPathLocation, UriLocation, 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;
+    },
+});
+export { ElementId } from "./ElementId.js";

package/esm/util/types/util.d.ts

@@ -0,0 +1,6 @@
+import type React from 'react';
+import type PluginManager from '../../PluginManager.ts';
+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/esm/util/types/util.js

@@ -0,0 +1 @@
+export {};

package/esm/util/useFeatureSequence.d.ts

@@ -0,0 +1,19 @@
+import type { AbstractSessionModel, Feature } from './index.ts';
+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/esm/util/useFeatureSequence.js

@@ -0,0 +1,87 @@
+import { useEffect, useMemo, useState } from 'react';
+import { fetchSeq } from "./fetchSeq.js";
+const BPLIMIT = 20_000_000;
+export function useFeatureSequence({ session, feature, upDownBp, forceLoad, assemblyName, shouldFetch = true, }) {
+    const [sequence, setSequence] = useState();
+    const [error, setError] = useState();
+    const [loading, setLoading] = useState(false);
+    const key = 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]);
+    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([
+                    fetchSeq({
+                        start,
+                        end,
+                        refName,
+                        assemblyName,
+                        session: session,
+                    }),
+                    fetchSeq({
+                        start: Math.max(0, b),
+                        end: start,
+                        refName,
+                        assemblyName,
+                        session: session,
+                    }),
+                    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/esm/util/useMeasure.js

@@ -0,0 +1,30 @@
+import { useEffect, useRef, useState } from 'react';
+export default function useMeasure() {
+    const ref = useRef(null);
+    const [dims, setDims] = useState({
+        width: undefined,
+        height: undefined,
+    });
+    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/esm/util/when.js

@@ -0,0 +1 @@
+export { when } from 'mobx';