@jbrowse/plugin-sequence 2.16.1 → 2.18.0

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -1,28 +1,29 @@
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { IndexedFasta } from '@gmod/indexedfasta';
-import { BaseSequenceAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, updateStatus2 } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
-import AbortablePromiseCache from '@gmod/abortable-promise-cache';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 200 }),
-            fill: async (args, signal) => {
+            fill: async (args) => {
                 const { refName, start, end, fasta } = args;
-                return fasta.getSequence(refName, start, end, { ...args, signal });
+                return fasta.getSequence(refName, start, end);
             },
         });
     }
-    async getRefNames(opts) {
+    async getRefNames(_opts) {
         const { fasta } = await this.setup();
-        return fasta.getSequenceNames(opts);
+        return fasta.getSequenceNames();
     }
-    async getRegions(opts) {
+    async getRegions(_opts) {
         const { fasta } = await this.setup();
-        const seqSizes = await fasta.getSequenceSizes(opts);
+        const seqSizes = await fasta.getSequenceSizes();
         return Object.keys(seqSizes).map(refName => ({
             refName,
             start: 0,
@@ -55,40 +56,45 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
         return this.setupP;
     }
     getFeatures(region, opts) {
+        const { statusCallback = () => { }, stopToken } = opts || {};
         const { refName, start, end } = region;
         return ObservableCreate(async (observer) => {
-            const { fasta } = await this.setup();
-            const size = await fasta.getSequenceSize(refName, opts);
-            const regionEnd = Math.min(size, 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, fasta }, 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 },
-                }));
-            }
+            await updateStatus2('Downloading sequence', statusCallback, stopToken, async () => {
+                const { fasta } = await this.setup();
+                const size = await fasta.getSequenceSize(refName);
+                const regionEnd = Math.min(size, 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,
+                    };
+                    checkStopToken(stopToken);
+                    chunks.push(await this.seqCache.get(JSON.stringify(r), { ...r, fasta }));
+                }
+                const seq = chunks
+                    .filter(f => !!f)
+                    .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 foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/IndexedFastaAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     faiLocation: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: string;
         type: string;

package/esm/IndexedFastaAdapter/configSchema.js

@@ -1,26 +1,14 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config IndexedFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const IndexedFastaAdapter = ConfigurationSchema('IndexedFastaAdapter', {
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',

package/esm/IndexedFastaAdapter/index.d.ts

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

package/esm/IndexedFastaAdapter/index.js

@@ -1,13 +1,15 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default function IndexedFastaAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'IndexedFastaAdapter',
-        displayName: 'Indexed FASTA adapter',
-        configSchema,
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'IndexedFastaAdapter',
+            displayName: 'Indexed FASTA adapter',
+            configSchema,
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
+        });
+    });
 }

package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -1,7 +1,4 @@
 export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         height: {
             type: string;

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema';
-/**
- * #config LinearReferenceSequenceDisplay
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', {
-    /**
-     * #slot
-     */
     renderer: divSequenceRendererConfigSchema,
 }, { explicitIdentifier: 'displayId', explicitlyTyped: true });

package/esm/LinearReferenceSequenceDisplay/index.d.ts

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

package/esm/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;
@@ -55,15 +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;
-            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;
@@ -191,6 +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;
 } & {
@@ -228,67 +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;
@@ -309,21 +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;
@@ -347,15 +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;
-            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;
@@ -392,8 +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/esm/LinearReferenceSequenceDisplay/model.js

@@ -1,76 +1,36 @@
-import { addDisposer, types } from 'mobx-state-tree';
-import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
-import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
-import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { getContainingTrack, getContainingView } from '@jbrowse/core/util';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import { autorun } from 'mobx';
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
+import { addDisposer, types } from 'mobx-state-tree';
 export function modelFactory(configSchema) {
     return types
         .compose('LinearReferenceSequenceDisplay', BaseLinearDisplay, types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearReferenceSequenceDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         showForward: true,
-        /**
-         * #property
-         */
         showReverse: true,
-        /**
-         * #property
-         */
         showTranslation: true,
     }))
         .volatile(() => ({
-        /**
-         * #property
-         */
         rowHeight: 15,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get sequenceType() {
             return getConf(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;
@@ -84,9 +44,6 @@ export function modelFactory(configSchema) {
         .views(self => {
         const { renderProps: superRenderProps } = self;
         return {
-            /**
-             * #method
-             */
             renderProps() {
                 const { rpcDriverName, showForwardActual, showReverseActual, showTranslationActual, rowHeight, sequenceHeight, sequenceType, } = self;
                 return {
@@ -105,36 +62,21 @@ export function modelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
-        regionCannotBeRendered( /* region */) {
+        regionCannotBeRendered() {
             const view = 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;
         },
@@ -151,9 +93,6 @@ export function modelFactory(configSchema) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         trackMenuItems() {
             return [
                 ...(self.sequenceType === 'dna'

package/esm/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;