@jbrowse/plugin-sequence 1.7.11 → 2.1.0

package/esm/GCContentAdapter/GCContentAdapter.js

@@ -0,0 +1,97 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { toArray } from 'rxjs/operators';
+export default class default_1 extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.windowSize = 1000;
+        this.windowDelta = 1000;
+        this.gcMode = 'content';
+    }
+    async configure() {
+        var _a;
+        // instantiate the sequence adapter
+        const sequenceAdapter = readConfObject(this.config, 'sequenceAdapter');
+        const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, sequenceAdapter));
+        if (!dataAdapter) {
+            throw new Error('Error getting subadapter');
+        }
+        return dataAdapter.dataAdapter;
+    }
+    async getRefNames() {
+        const sequenceAdapter = await this.configure();
+        return sequenceAdapter.getRefNames();
+    }
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(query, opts) {
+        this.windowSize = 1000;
+        this.windowDelta = 1000;
+        this.gcMode = 'content';
+        return ObservableCreate(async (observer) => {
+            var _a;
+            const sequenceAdapter = await this.configure();
+            const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
+            const f = this.windowSize === 1;
+            let { start: queryStart, end: queryEnd } = query;
+            queryStart = Math.max(0, queryStart - hw);
+            queryEnd += hw;
+            if (queryEnd < 0 || queryStart > queryEnd) {
+                observer.complete();
+                return;
+            }
+            const ret = sequenceAdapter.getFeatures({
+                ...query,
+                start: queryStart,
+                end: queryEnd,
+            });
+            const feats = await ret.pipe(toArray()).toPromise();
+            const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
+            for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
+                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
+                let nc = 0;
+                let ng = 0;
+                let len = 0;
+                for (let j = 0; j < r.length; j++) {
+                    if (r[j] === 'c' || r[j] === 'C') {
+                        nc++;
+                    }
+                    else if (r[j] === 'g' || r[j] === 'G') {
+                        ng++;
+                    }
+                    if (r[j] !== 'N') {
+                        len++;
+                    }
+                }
+                const pos = queryStart;
+                let score;
+                if (this.gcMode === 'content') {
+                    score = (ng + nc) / (len || 1);
+                }
+                else if (this.gcMode === 'skew') {
+                    score = (ng - nc) / (ng + nc || 1);
+                }
+                observer.next(new SimpleFeature({
+                    uniqueId: `${this.id}_${pos + i}`,
+                    start: pos + i,
+                    end: pos + i + this.windowDelta,
+                    score,
+                }));
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+default_1.capabilities = ['hasLocalStats'];
+//# sourceMappingURL=GCContentAdapter.js.map

package/esm/GCContentAdapter/GCContentAdapter.js.map

@@ -0,0 +1 @@
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package/esm/GCContentAdapter/configSchema.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/GCContentAdapter/configSchema.js

@@ -0,0 +1,7 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default (pluginManager) => {
+    return ConfigurationSchema('GCContentAdapter', {
+        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    }, { explicitlyTyped: true });
+};
+//# sourceMappingURL=configSchema.js.map

package/esm/GCContentAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/GCContentAdapter/index.d.ts

@@ -0,0 +1,6 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => {
+    configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    getAdapterClass: () => Promise<typeof import("./GCContentAdapter").default>;
+};
+export default _default;

package/esm/GCContentAdapter/index.js

@@ -0,0 +1,8 @@
+import configSchemaF from './configSchema';
+export default (pluginManager) => {
+    return {
+        configSchema: pluginManager.load(configSchemaF),
+        getAdapterClass: () => import('./GCContentAdapter').then(r => r.default),
+    };
+};
+//# sourceMappingURL=index.js.map

package/esm/GCContentAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -0,0 +1,27 @@
+import { IndexedFasta } from '@gmod/indexedfasta';
+import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseSequenceAdapter {
+    protected fasta: IndexedFasta;
+    protected header?: Promise<string>;
+    private seqCache;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getRegions(opts?: BaseOptions): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    getHeader(): Promise<string | null>;
+    getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -0,0 +1,90 @@
+import { IndexedFasta } from '@gmod/indexedfasta';
+import { BaseSequenceAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { SimpleFeature } from '@jbrowse/core/util';
+import AbortablePromiseCache from 'abortable-promise-cache';
+import LRU from '@jbrowse/core/util/QuickLRU';
+export default class extends BaseSequenceAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.seqCache = new AbortablePromiseCache({
+            cache: new LRU({ maxSize: 200 }),
+            fill: async (args, signal) => {
+                const { refName, start, end } = args;
+                return this.fasta.getSequence(refName, start, end, { ...args, signal });
+            },
+        });
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        const fastaOpts = {
+            fasta: openLocation(fastaLocation, this.pluginManager),
+            fai: openLocation(faiLocation, this.pluginManager),
+        };
+        this.fasta = new IndexedFasta(fastaOpts);
+    }
+    getRefNames(opts) {
+        return this.fasta.getSequenceNames(opts);
+    }
+    async getRegions(opts) {
+        const seqSizes = await this.fasta.getSequenceSizes(opts);
+        return Object.keys(seqSizes).map(refName => ({
+            refName,
+            start: 0,
+            end: seqSizes[refName],
+        }));
+    }
+    async getHeader() {
+        if (this.header) {
+            return this.header;
+        }
+        const loc = this.getConf('metadataLocation');
+        if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
+            return null;
+        }
+        this.header = openLocation(loc)
+            .readFile('utf8')
+            .catch(e => {
+            this.header = undefined;
+            throw e;
+        });
+        return this.header;
+    }
+    getFeatures(region, opts) {
+        const { refName, start, end } = region;
+        return ObservableCreate(async (observer) => {
+            const size = await this.fasta.getSequenceSize(refName, opts);
+            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const chunks = [];
+            const chunkSize = 128000;
+            const s = start - (start % chunkSize);
+            const e = end + (chunkSize - (end % chunkSize));
+            for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
+                const r = {
+                    refName,
+                    start: chunkStart,
+                    end: chunkStart + chunkSize,
+                };
+                chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+            }
+            const seq = (await Promise.all(chunks))
+                .join('')
+                .slice(start - s)
+                .slice(0, end - start);
+            if (seq) {
+                observer.next(new SimpleFeature({
+                    id: `${refName} ${start}-${regionEnd}`,
+                    data: { refName, start, end: regionEnd, seq },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=IndexedFastaAdapter.js.map

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -0,0 +1 @@
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package/esm/IndexedFastaAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/IndexedFastaAdapter/configSchema.js

@@ -0,0 +1,20 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('IndexedFastaAdapter', {
+    fastaLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
+    },
+    faiLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
+    },
+    metadataLocation: {
+        description: 'Optional metadata file',
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/fa.metadata.yaml',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/IndexedFastaAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/IndexedFastaAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/IndexedFastaAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/IndexedFastaAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -0,0 +1 @@
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -0,0 +1,4 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { configSchema as divSequenceRendererConfigSchema } from '../DivSequenceRenderer';
+export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', { renderer: divSequenceRendererConfigSchema }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,YAAY,IAAI,+BAA+B,EAAE,MAAM,wBAAwB,CAAA;AAExF,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,+BAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/esm/LinearReferenceSequenceDisplay/index.d.ts

@@ -0,0 +1,2 @@
+export { configSchema } from './configSchema';
+export { modelFactory } from './model';

package/esm/LinearReferenceSequenceDisplay/index.js

@@ -0,0 +1,3 @@
+export { configSchema } from './configSchema';
+export { modelFactory } from './model';
+//# sourceMappingURL=index.js.map

package/esm/LinearReferenceSequenceDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAA"}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -0,0 +1,210 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+export declare function modelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        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>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    showForward: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showReverse: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTranslation: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    height: import("mobx-state-tree").IType<number | undefined, number, number>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: any;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    setMessage(message: string): void;
+    afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<{}>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    renderProps(): any;
+    regionCannotBeRendered(): "Zoom in to see sequence" | undefined;
+    readonly rendererTypeName: any;
+} & {
+    toggleShowForward(): void;
+    toggleShowReverse(): void;
+    toggleShowTranslation(): void;
+} & {
+    trackMenuItems(): {
+        label: string;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+    }[];
+}, import("mobx-state-tree")._NotCustomized, {
+    type: string;
+    height: number;
+    id: string;
+    rpcDriverName: string | undefined;
+    userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
+} & import("mobx-state-tree")._NotCustomized>;

package/esm/LinearReferenceSequenceDisplay/model.js

@@ -0,0 +1,83 @@
+import { types } from 'mobx-state-tree';
+import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
+import { ConfigurationReference, } from '@jbrowse/core/configuration';
+import { getContainingView } from '@jbrowse/core/util';
+export function modelFactory(configSchema) {
+    return types
+        .compose('LinearReferenceSequenceDisplay', BaseLinearDisplay, types.model({
+        type: types.literal('LinearReferenceSequenceDisplay'),
+        configuration: ConfigurationReference(configSchema),
+        showForward: types.optional(types.boolean, true),
+        showReverse: types.optional(types.boolean, true),
+        showTranslation: types.optional(types.boolean, true),
+        height: 180,
+    }))
+        .views(self => {
+        const { renderProps: superRenderProps } = self;
+        return {
+            renderProps() {
+                const { showForward, showReverse, showTranslation } = self;
+                return {
+                    ...superRenderProps(),
+                    rpcDriverName: self.rpcDriverName,
+                    config: self.configuration.renderer,
+                    showForward,
+                    showReverse,
+                    showTranslation,
+                };
+            },
+            regionCannotBeRendered( /* region */) {
+                const view = getContainingView(self);
+                if (view && view.bpPerPx >= 1) {
+                    return 'Zoom in to see sequence';
+                }
+                return undefined;
+            },
+            get rendererTypeName() {
+                return self.configuration.renderer.type;
+            },
+        };
+    })
+        .actions(self => ({
+        toggleShowForward() {
+            self.showForward = !self.showForward;
+        },
+        toggleShowReverse() {
+            self.showReverse = !self.showReverse;
+        },
+        toggleShowTranslation() {
+            self.showTranslation = !self.showTranslation;
+        },
+    }))
+        .views(self => ({
+        trackMenuItems() {
+            return [
+                {
+                    label: 'Show forward',
+                    type: 'checkbox',
+                    checked: self.showForward,
+                    onClick: () => {
+                        self.toggleShowForward();
+                    },
+                },
+                {
+                    label: 'Show reverse',
+                    type: 'checkbox',
+                    checked: self.showReverse,
+                    onClick: () => {
+                        self.toggleShowReverse();
+                    },
+                },
+                {
+                    label: 'Show translation',
+                    type: 'checkbox',
+                    checked: self.showTranslation,
+                    onClick: () => {
+                        self.toggleShowTranslation();
+                    },
+                },
+            ];
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map

package/esm/LinearReferenceSequenceDisplay/model.js.map

@@ -0,0 +1 @@
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