@jbrowse/plugin-sequence 2.17.0 → 2.18.0

package/dist/BgzipFastaAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurati
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     faiLocation: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurati
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: string;
         type: string;
@@ -30,9 +21,6 @@ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurati
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     gziLocation: {
         type: string;
         defaultValue: {

package/dist/BgzipFastaAdapter/configSchema.js

@@ -1,21 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BgzipFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter', {
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -23,9 +14,6 @@ const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAd
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',
@@ -34,9 +22,6 @@ const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAd
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     gziLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/BgzipFastaAdapter/index.d.ts

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

package/dist/BgzipFastaAdapter/index.js

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

package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,4 +1,5 @@
-import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class ChromSizesAdapter extends BaseAdapter implements RegionsAdapter {
     protected setupP?: Promise<Record<string, number>>;
     setupPre(): Promise<{

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -36,6 +36,6 @@ class ChromSizesAdapter extends BaseAdapter_1.BaseAdapter {
     getHeader() {
         return {};
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = ChromSizesAdapter;

package/dist/ChromSizesAdapter/configSchema.d.ts

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

package/dist/ChromSizesAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config ChromSizesAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ChromSizesAdapter = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter', {
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/ChromSizesAdapter/index.d.ts

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

package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature, Region } from '@jbrowse/core/util';
-import { Theme } from '@mui/material';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature, Region } from '@jbrowse/core/util';
+import type { Theme } from '@mui/material';
 declare const DivSequenceRendering: (props: {
     exportSVG?: {
         rasterizeLayers: boolean;

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
 function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, theme, }) {
     var _a, _b;
     const normalizedFrame = Math.abs(frame) - 1;
@@ -49,7 +49,7 @@ function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqS
             return !(renderLetter || codonFill) ? null : (react_1.default.createElement(react_1.default.Fragment, { key: `${index}-${letter}` },
                 react_1.default.createElement("rect", { x: x, y: y, width: renderLetter
                         ? codonWidth
-                        : codonWidth + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }),
+                        : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }),
                 renderLetter ? (react_1.default.createElement("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
         })));
 }
@@ -63,13 +63,11 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
     const w = Math.max((rightPx - leftPx) / len, 0.8);
     return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map((letter, index) => {
         const color = sequenceType === 'dna'
-            ? // @ts-expect-error
+            ?
                 theme.palette.bases[letter.toUpperCase()]
             : undefined;
         const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-        return (
-        /* biome-ignore lint/suspicious/noArrayIndexKey: */
-        react_1.default.createElement(react_1.default.Fragment, { key: `${letter}-${index}` },
+        return (react_1.default.createElement(react_1.default.Fragment, { key: `${letter}-${index}` },
             react_1.default.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
             render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
     })));
@@ -86,13 +84,10 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
     if (!seq) {
         return null;
     }
-    // incrementer for the y-position of the current sequence being rendered
-    // (applies to both translation rows and dna rows)
     let currY = -rowHeight;
     const showSequence = bpPerPx <= 1;
     const forwardFrames = showTranslation && showForward ? [3, 2, 1] : [];
     const reverseFrames = showTranslation && showReverse ? [-1, -2, -3] : [];
-    // if region.reversed, the forward translation is on bottom, reverse on top
     const [topFrames, bottomFrames] = region.reversed
         ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
         : [forwardFrames, reverseFrames];
@@ -104,7 +99,6 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
     return exportSVG ? (children) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
-            // use block because svg by default is inline, which adds a margin
             display: 'block',
             width,
             height: totalHeight,

package/dist/DivSequenceRenderer/configSchema.d.ts

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

package/dist/DivSequenceRenderer/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config DivSequenceRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DivSequenceRenderer = (0, configuration_1.ConfigurationSchema)('DivSequenceRenderer', {
-    /**
-     * #slot
-     */
     height: {
         type: 'number',
         description: 'height in pixels of each line of sequence',

package/dist/DivSequenceRenderer/index.d.ts

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

package/dist/DivSequenceRenderer/index.js

@@ -7,7 +7,6 @@ exports.default = DivSequenceRendererF;
 const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
 const DivSequenceRendering_1 = __importDefault(require("./components/DivSequenceRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-/* adjust in both directions */
 class DivSequenceRenderer extends FeatureRendererType_1.default {
     constructor() {
         super(...arguments);

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -1,14 +1,15 @@
 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 { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     protected setupP?: Promise<{
         fasta: IndexedFasta;
     }>;
     private seqCache;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getRegions(opts?: BaseOptions): Promise<{
+    getRefNames(_opts?: BaseOptions): Promise<string[]>;
+    getRegions(_opts?: BaseOptions): Promise<{
         refName: string;
         start: number;
         end: number;
@@ -21,10 +22,5 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
         fasta: IndexedFasta;
     }>;
     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 foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -3,31 +3,32 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const indexedfasta_1 = require("@gmod/indexedfasta");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new abortable_promise_cache_1.default({
             cache: new QuickLRU_1.default({ 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,
@@ -60,41 +61,46 @@ class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
         return this.setupP;
     }
     getFeatures(region, opts) {
+        const { statusCallback = () => { }, stopToken } = opts || {};
         const { refName, start, end } = region;
         return (0, rxjs_1.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 util_1.SimpleFeature({
-                    id: `${refName} ${start}-${regionEnd}`,
-                    data: { refName, start, end: regionEnd, seq },
-                }));
-            }
+            await (0, util_1.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,
+                    };
+                    (0, stopToken_1.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 util_1.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() { }
 }
 exports.default = IndexedFastaAdapter;

package/dist/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/dist/IndexedFastaAdapter/configSchema.js

@@ -1,28 +1,16 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config IndexedFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const IndexedFastaAdapter = (0, configuration_1.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/dist/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/dist/IndexedFastaAdapter/index.js

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

package/dist/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/dist/LinearReferenceSequenceDisplay/configSchema.js

@@ -6,13 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema_1 = __importDefault(require("../DivSequenceRenderer/configSchema"));
-/**
- * #config LinearReferenceSequenceDisplay
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', {
-    /**
-     * #slot
-     */
     renderer: configSchema_1.default,
 }, { explicitIdentifier: 'displayId', explicitlyTyped: true });

package/dist/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;