@jbrowse/plugin-sequence 2.17.0 → 2.18.0

package/dist/TwoBitAdapter/TwoBitAdapter.js

@@ -3,18 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const twobit_1 = require("@gmod/twobit");
+const configuration_1 = require("@jbrowse/core/configuration");
 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 simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const twobit_1 = require("@gmod/twobit");
-const configuration_1 = require("@jbrowse/core/configuration");
 class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
     async initChromSizes() {
         const conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
-        // check against default and empty in case someone makes the field blank in
-        // config editor, may want better way to check "optional config slots" in
-        // future
         if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
             const file = (0, io_1.openLocation)(conf, this.pluginManager);
             const data = await file.readFile('utf8');
@@ -28,23 +25,31 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
         }
         return undefined;
     }
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const pm = this.pluginManager;
-        this.chromSizesData = this.initChromSizes();
-        this.twobit = new twobit_1.TwoBitFile({
-            filehandle: (0, io_1.openLocation)(this.getConf('twoBitLocation'), pm),
-        });
+    async setupPre() {
+        return {
+            twobit: new twobit_1.TwoBitFile({
+                filehandle: (0, io_1.openLocation)(this.getConf('twoBitLocation'), this.pluginManager),
+            }),
+            chromSizesData: await this.initChromSizes(),
+        };
     }
-    async getRefNames() {
-        const chromSizesData = await this.chromSizesData;
-        if (chromSizesData) {
-            return Object.keys(chromSizesData);
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        return this.twobit.getSequenceNames();
+        return this.setupP;
+    }
+    async getRefNames() {
+        const { chromSizesData, twobit } = await this.setup();
+        return chromSizesData
+            ? Object.keys(chromSizesData)
+            : twobit.getSequenceNames();
     }
     async getRegions() {
-        const chromSizesData = await this.chromSizesData;
+        const { chromSizesData, twobit } = await this.setup();
         if (chromSizesData) {
             return Object.keys(chromSizesData).map(refName => ({
                 refName,
@@ -52,23 +57,21 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
                 end: chromSizesData[refName],
             }));
         }
-        const refSizes = await this.twobit.getSequenceSizes();
-        return Object.keys(refSizes).map(refName => ({
-            refName,
-            start: 0,
-            end: refSizes[refName],
-        }));
+        else {
+            const refSizes = await twobit.getSequenceSizes();
+            return Object.keys(refSizes).map(refName => ({
+                refName,
+                start: 0,
+                end: refSizes[refName],
+            }));
+        }
     }
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures({ refName, start, end }) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const size = await this.twobit.getSequenceSize(refName);
+            const { twobit } = await this.setup();
+            const size = await twobit.getSequenceSize(refName);
             const regionEnd = size !== undefined ? Math.min(size, end) : end;
-            const seq = await this.twobit.getSequence(refName, start, regionEnd);
+            const seq = await twobit.getSequence(refName, start, regionEnd);
             if (seq) {
                 observer.next(new simpleFeature_1.default({
                     id: `${refName} ${start}-${regionEnd}`,
@@ -78,11 +81,6 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
             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 = TwoBitAdapter;

package/dist/TwoBitAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     twoBitLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: string;
         defaultValue: {

package/dist/TwoBitAdapter/configSchema.js

@@ -1,21 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config TwoBitAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const TwoBitAdapter = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
-    /**
-     * #slot
-     */
     twoBitLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/TwoBitAdapter/index.d.ts

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

package/dist/UnindexedFastaAdapter/UnindexedFastaAdapter.d.ts

@@ -1,6 +1,7 @@
-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';
 declare function parseSmallFasta(text: string): Map<string, {
     readonly description: string;
     readonly sequence: string;

package/dist/UnindexedFastaAdapter/UnindexedFastaAdapter.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
 function parseSmallFasta(text) {
     return new Map(text
         .split('>')
@@ -82,6 +82,6 @@ class UnindexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = UnindexedFastaAdapter;

package/dist/UnindexedFastaAdapter/configSchema.d.ts

@@ -4,9 +4,6 @@ declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configu
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -14,9 +11,6 @@ declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configu
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: string;
         type: string;

package/dist/UnindexedFastaAdapter/configSchema.js

@@ -1,19 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config UnindexedFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const UnindexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('UnindexedFastaAdapter', {
     rewriteRefNames: {
         type: 'string',
         defaultValue: '',
         contextVariable: ['refName'],
     },
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -21,9 +15,6 @@ const UnindexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('Unindexe
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',

package/dist/UnindexedFastaAdapter/index.d.ts

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

package/dist/UnindexedFastaAdapter/index.js

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

package/dist/createExtensionPoints.d.ts

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

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class SequencePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,15 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const TwoBitAdapter_1 = __importDefault(require("./TwoBitAdapter"));
-const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
 const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
 const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
+const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
 const IndexedFastaAdapter_1 = __importDefault(require("./IndexedFastaAdapter"));
-const UnindexedFastaAdapter_1 = __importDefault(require("./UnindexedFastaAdapter"));
-const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
-const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
 const LinearReferenceSequenceDisplay_1 = __importDefault(require("./LinearReferenceSequenceDisplay"));
+const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
+const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
+const TwoBitAdapter_1 = __importDefault(require("./TwoBitAdapter"));
+const UnindexedFastaAdapter_1 = __importDefault(require("./UnindexedFastaAdapter"));
 const createExtensionPoints_1 = __importDefault(require("./createExtensionPoints"));
 class SequencePlugin extends Plugin_1.default {
     constructor() {

package/esm/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/esm/BgzipFastaAdapter/configSchema.js

@@ -1,19 +1,10 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BgzipFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -21,9 +12,6 @@ const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',
@@ -32,9 +20,6 @@ const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     gziLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/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/esm/BgzipFastaAdapter/index.js

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

package/esm/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/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,4 +1,4 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 export default class ChromSizesAdapter extends BaseAdapter {
     async setupPre() {
@@ -34,5 +34,5 @@ export default class ChromSizesAdapter extends BaseAdapter {
     getHeader() {
         return {};
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/ChromSizesAdapter/configSchema.d.ts

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

package/esm/ChromSizesAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config ChromSizesAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ChromSizesAdapter = ConfigurationSchema('ChromSizesAdapter', {
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/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/esm/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/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { bpSpanPx, complement, defaultCodonTable, defaultStarts, defaultStops, generateCodonTable, revcom, } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { bpSpanPx, revcom, complement, defaultStarts, defaultStops, defaultCodonTable, generateCodonTable, } from '@jbrowse/core/util';
 function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, theme, }) {
     var _a, _b;
     const normalizedFrame = Math.abs(frame) - 1;
@@ -44,7 +44,7 @@ function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqS
             return !(renderLetter || codonFill) ? null : (React.createElement(React.Fragment, { key: `${index}-${letter}` },
                 React.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.createElement("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
         })));
 }
@@ -58,13 +58,11 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
     const w = Math.max((rightPx - leftPx) / len, 0.8);
     return (React.createElement(React.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.createElement(React.Fragment, { key: `${letter}-${index}` },
+        return (React.createElement(React.Fragment, { key: `${letter}-${index}` },
             React.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
             render ? (React.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));
     })));
@@ -81,13 +79,10 @@ 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];
@@ -99,7 +94,6 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
     return exportSVG ? (children) : (React.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/esm/DivSequenceRenderer/configSchema.d.ts

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

package/esm/DivSequenceRenderer/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config DivSequenceRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DivSequenceRenderer = ConfigurationSchema('DivSequenceRenderer', {
-    /**
-     * #slot
-     */
     height: {
         type: 'number',
         description: 'height in pixels of each line of sequence',

package/esm/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/esm/DivSequenceRenderer/index.js

@@ -1,7 +1,6 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import ReactComponent from './components/DivSequenceRendering';
 import configSchema from './configSchema';
-/* adjust in both directions */
 class DivSequenceRenderer extends FeatureRendererType {
     constructor() {
         super(...arguments);

package/esm/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;
 }