@jbrowse/plugin-sequence 2.17.0 → 2.18.0

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -1,8 +1,4 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
+import type { 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>;
@@ -15,23 +11,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     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" /**
-             * #property
-             */).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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -55,17 +40,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement /**
-             * #method
-             */;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -193,6 +170,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -230,67 +208,25 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
 } & {
-    /**
-     * #property
-     */
     rowHeight: number;
 } & {
-    /**
-     * #getter
-     */
     readonly sequenceType: any;
-    /**
-     * #getter
-     * showReverse setting, it is NOT disabled for non-dna sequences
-     */
     readonly showForwardActual: boolean;
-    /**
-     * #getter
-     * showReverse setting, is disabled for non-dna sequences
-     */
     readonly showReverseActual: boolean;
-    /**
-     * #getter
-     * showTranslation setting is disabled for non-dna sequences
-     */
     readonly showTranslationActual: boolean;
 } & {
-    /**
-     * #getter
-     */
     readonly sequenceHeight: number;
 } & {
-    /**
-     * #method
-     */
     renderProps(): any;
 } & {
-    /**
-     * #method
-     */
     regionCannotBeRendered(): "Zoom in to see sequence" | undefined;
-    /**
-     * #getter
-     */
     readonly rendererTypeName: any;
 } & {
-    /**
-     * #action
-     */
     toggleShowForward(): void;
-    /**
-     * #action
-     */
     toggleShowReverse(): void;
-    /**
-     * #action
-     */
     toggleShowTranslation(): void;
     afterAttach(): void;
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): {
         label: string;
         type: string;
@@ -311,21 +247,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -349,17 +276,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement /**
-             * #method
-             */;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -396,8 +315,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: string;
     id: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    heightPreConfig: number | undefined;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearReferenceSequenceDisplay/model.js

@@ -1,79 +1,39 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.modelFactory = modelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configuration_1 = require("@jbrowse/core/configuration");
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_1 = require("mobx");
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
+const mobx_state_tree_1 = require("mobx-state-tree");
 function modelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearReferenceSequenceDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearReferenceSequenceDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
         showForward: true,
-        /**
-         * #property
-         */
         showReverse: true,
-        /**
-         * #property
-         */
         showTranslation: true,
     }))
         .volatile(() => ({
-        /**
-         * #property
-         */
         rowHeight: 15,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get sequenceType() {
             return (0, configuration_1.getConf)((0, util_1.getContainingTrack)(self), 'sequenceType');
         },
-        /**
-         * #getter
-         * showReverse setting, it is NOT disabled for non-dna sequences
-         */
         get showForwardActual() {
             return self.showForward;
         },
-        /**
-         * #getter
-         * showReverse setting, is disabled for non-dna sequences
-         */
         get showReverseActual() {
             return this.sequenceType === 'dna' ? self.showReverse : false;
         },
-        /**
-         * #getter
-         * showTranslation setting is disabled for non-dna sequences
-         */
         get showTranslationActual() {
             return this.sequenceType === 'dna' ? self.showTranslation : false;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get sequenceHeight() {
             const { rowHeight, showTranslationActual, showReverseActual, showForwardActual, } = self;
             const r1 = showReverseActual && showTranslationActual ? rowHeight * 3 : 0;
@@ -87,9 +47,6 @@ function modelFactory(configSchema) {
         .views(self => {
         const { renderProps: superRenderProps } = self;
         return {
-            /**
-             * #method
-             */
             renderProps() {
                 const { rpcDriverName, showForwardActual, showReverseActual, showTranslationActual, rowHeight, sequenceHeight, sequenceType, } = self;
                 return {
@@ -108,36 +65,21 @@ function modelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
-        regionCannotBeRendered( /* region */) {
+        regionCannotBeRendered() {
             const view = (0, util_1.getContainingView)(self);
             return view.bpPerPx > 3 ? 'Zoom in to see sequence' : undefined;
         },
-        /**
-         * #getter
-         */
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         toggleShowForward() {
             self.showForward = !self.showForward;
         },
-        /**
-         * #action
-         */
         toggleShowReverse() {
             self.showReverse = !self.showReverse;
         },
-        /**
-         * #action
-         */
         toggleShowTranslation() {
             self.showTranslation = !self.showTranslation;
         },
@@ -154,9 +96,6 @@ function modelFactory(configSchema) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         trackMenuItems() {
             return [
                 ...(self.sequenceType === 'dna'

package/dist/ReferenceSequenceTrack/configSchema.d.ts

@@ -1,60 +1,34 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * configuration for track adapter
-     */
     adapter: import("mobx-state-tree").IAnyModelType;
-    /**
-     * #slot
-     * configuration for the displays e.g. LinearReferenceSequenceDisplay
-     */
     displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    /**
-     * #slot
-     */
     name: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     sequenceType: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     description: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     metadata: {
         type: string;
         description: string;
         defaultValue: {};
     };
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot formatAbout.config
-         */
         config: {
             type: string;
             description: string;
             defaultValue: {};
             contextVariable: string[];
         };
-        /**
-         * #slot formatAbout.hideUris
-         */
         hideUris: {
             type: string;
             defaultValue: boolean;

package/dist/ReferenceSequenceTrack/configSchema.js

@@ -1,73 +1,40 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-// Note: this is primarily a copy of createBaseTrackConfig, except with a
-// subset of the config slots, to avoid including fields that don't make sense
-// for the ReferenceSequenceTrack
-/**
- * #config ReferenceSequenceTrack
- * used to display base level DNA sequence tracks
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
 function createReferenceSeqTrackConfig(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('ReferenceSequenceTrack', {
-        /**
-         * #slot
-         * configuration for track adapter
-         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        /**
-         * #slot
-         * configuration for the displays e.g. LinearReferenceSequenceDisplay
-         */
         displays: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('display')),
-        /**
-         * #slot
-         */
         name: {
             type: 'string',
             description: 'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
             defaultValue: '',
         },
-        /**
-         * #slot
-         */
         sequenceType: {
             type: 'string',
             description: 'either dna or pep',
             defaultValue: 'dna',
         },
-        /**
-         * #slot
-         */
         description: {
             description: 'a description of the track',
             type: 'string',
             defaultValue: '',
         },
-        /**
-         * #slot
-         */
         metadata: {
             type: 'frozen',
             description: 'anything to add about this track',
             defaultValue: {},
         },
         formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
-            /**
-             * #slot formatAbout.config
-             */
             config: {
                 type: 'frozen',
                 description: 'formats configuration in about dialog',
                 defaultValue: {},
                 contextVariable: ['config'],
             },
-            /**
-             * #slot formatAbout.hideUris
-             */
             hideUris: {
                 type: 'boolean',
                 defaultValue: false,
@@ -79,9 +46,6 @@ function createReferenceSeqTrackConfig(pluginManager) {
             const displayTypes = new Set();
             const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
-                // Gets the displays on the track snapshot and the possible displays
-                // from the track type and adds any missing possible displays to the
-                // snapshot
                 displays.forEach((d) => d && displayTypes.add(d.type));
                 const trackType = pluginManager.getTrackType(snap.type);
                 trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes.forEach(displayType => {
@@ -95,10 +59,6 @@ function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
-        /**
-         * #identifier
-         * all tracks have a globally unique 'trackId'
-         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/dist/ReferenceSequenceTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ReferenceSequenceTrackF(pluginManager: PluginManager): void;

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
-const operators_1 = require("rxjs/operators");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const rxjs_2 = require("rxjs");
+const operators_1 = require("rxjs/operators");
 class SequenceSearchAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a;

package/dist/SequenceSearchAdapter/configSchema.d.ts

@@ -1,36 +1,21 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     search: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         defaultValue: null;
     };
-    /**
-     * #slot
-     */
     searchForward: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     searchReverse: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     caseInsensitive: {
         type: string;
         defaultValue: boolean;

package/dist/SequenceSearchAdapter/configSchema.js

@@ -1,43 +1,25 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config SequenceSearchAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('SequenceSearchAdapter', {
-    /**
-     * #slot
-     */
     search: {
         type: 'string',
         defaultValue: '',
         description: 'Search string or regex to search for',
     },
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: 'frozen',
         defaultValue: null,
     },
-    /**
-     * #slot
-     */
     searchForward: {
         type: 'boolean',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     searchReverse: {
         type: 'boolean',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     caseInsensitive: {
         type: 'boolean',
         defaultValue: true,

package/dist/SequenceSearchAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SequenceSearchAdapterF(pluginManager: PluginManager): void;

package/dist/SequenceSearchAdapter/index.js

@@ -30,13 +30,15 @@ exports.default = SequenceSearchAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function SequenceSearchAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'SequenceSearchAdapter',
-        displayName: 'Sequence search adapter',
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'SequenceSearchAdapter',
+            displayName: 'Sequence search adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
+        });
+    });
 }

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,26 +1,29 @@
+import { TwoBitFile } from '@gmod/twobit';
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class TwoBitAdapter extends BaseSequenceAdapter {
-    private twobit;
-    protected chromSizesData: Promise<Record<string, number> | undefined>;
+    protected setupP?: Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: Record<string, number> | undefined;
+    }>;
     private initChromSizes;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    setupPre(): Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: {
+            [k: string]: number;
+        } | undefined;
+    }>;
+    setup(): Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: Record<string, number> | undefined;
+    }>;
     getRefNames(): Promise<string[]>;
-    getRegions(): Promise<NoAssemblyRegion[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
     getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
-    /**
-     * 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
-     */
     freeResources(): void;
 }