@jbrowse/plugin-sequence 2.13.0 → 2.14.0

package/dist/createExtensionPoints.js

@@ -15,7 +15,7 @@ function ExtensionPointsF(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);
@@ -42,7 +42,7 @@ function ExtensionPointsF(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);
@@ -69,7 +69,7 @@ function ExtensionPointsF(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);

package/dist/index.js

@@ -9,6 +9,7 @@ const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
 const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
 const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
 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"));
@@ -24,6 +25,7 @@ class SequencePlugin extends Plugin_1.default {
         (0, BgzipFastaAdapter_1.default)(pluginManager);
         (0, ChromSizesAdapter_1.default)(pluginManager);
         (0, IndexedFastaAdapter_1.default)(pluginManager);
+        (0, UnindexedFastaAdapter_1.default)(pluginManager);
         (0, SequenceSearchAdapter_1.default)(pluginManager);
         (0, ReferenceSequenceTrack_1.default)(pluginManager);
         (0, LinearReferenceSequenceDisplay_1.default)(pluginManager);

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -9,14 +9,14 @@ export default class ChromSizesAdapter extends BaseAdapter {
             .split(/\n|\r\n|\r/)
             .map(f => f.trim())
             .filter(f => !!f)
-            .map((line) => {
+            .map(line => {
             const [name, length] = line.split('\t');
             return [name, +length];
         }));
     }
     async setup() {
         if (!this.setupP) {
-            this.setupP = this.setupPre().catch(e => {
+            this.setupP = this.setupPre().catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -41,34 +41,36 @@ function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqS
                 : defaultStops.includes(codon)
                     ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
                     : undefined;
-            if (!(renderLetter || codonFill)) {
-                return null;
-            }
-            return (React.createElement(React.Fragment, { key: `${index}-${letter}` },
+            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' }),
                 renderLetter ? (React.createElement("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
         })));
 }
-function DNA(props) {
-    const { bpPerPx, region, feature, theme, height, seq, y } = props;
+function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq, y, }) {
     const render = 1 / bpPerPx >= 12;
-    const [leftPx, rightPx] = bpSpanPx(feature.get('start'), feature.get('end'), region, bpPerPx);
+    const s = feature.get('start');
+    const e = feature.get('end');
+    const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx);
     const reverse = region.reversed;
-    const len = feature.get('end') - feature.get('start');
+    const len = e - s;
     const w = Math.max((rightPx - leftPx) / len, 0.8);
     return (React.createElement(React.Fragment, null, seq.split('').map((letter, index) => {
-        // @ts-expect-error
-        const color = theme.palette.bases[letter.toUpperCase()];
+        const color = sequenceType === 'dna'
+            ? // @ts-expect-error
+                theme.palette.bases[letter.toUpperCase()]
+            : undefined;
         const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-        return (React.createElement(React.Fragment, { key: index },
+        return (
+        /* biome-ignore lint/suspicious/noArrayIndexKey: */
+        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));
     })));
 }
-function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, rowHeight, }) {
-    const [region] = regions;
+function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
+    const region = regions[0];
     const theme = createJBrowseTheme(configTheme);
     const codonTable = generateCodonTable(defaultCodonTable);
     const [feature] = [...features.values()];
@@ -82,7 +84,7 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
     // incrementer for the y-position of the current sequence being rendered
     // (applies to both translation rows and dna rows)
     let currY = -rowHeight;
-    const showDNA = bpPerPx <= 1;
+    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
@@ -91,8 +93,8 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
         : [forwardFrames, reverseFrames];
     return (React.createElement(React.Fragment, null,
         topFrames.map(index => (React.createElement(Translation, { key: `translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }))),
-        showForward && showDNA ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
-        showReverse && showDNA ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
+        showForward && showSequence ? (React.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
+        showReverse && showSequence ? (React.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
         bottomFrames.map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed })))));
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
@@ -106,7 +108,7 @@ function Wrapper({ exportSVG, width, totalHeight, children, }) {
 }
 const DivSequenceRendering = observer(function (props) {
     const { regions, bpPerPx, sequenceHeight } = props;
-    const [region] = regions;
+    const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
     return (React.createElement(Wrapper, { ...props, totalHeight: sequenceHeight, width: width },
         React.createElement(SequenceSVG, { ...props })));

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -47,7 +47,7 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     }
     async setup() {
         if (!this.setupP) {
-            this.setupP = this.setupPre().catch(e => {
+            this.setupP = this.setupPre().catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });
@@ -59,7 +59,7 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
         return ObservableCreate(async (observer) => {
             const { fasta } = await this.setup();
             const size = await fasta.getSequenceSize(refName, opts);
-            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const regionEnd = Math.min(size, end);
             const chunks = [];
             const chunkSize = 128000;
             const s = start - (start % chunkSize);

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -18,7 +18,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         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>;
+            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>;
@@ -123,7 +125,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
@@ -143,9 +145,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -232,6 +232,26 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
      * #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

package/esm/LinearReferenceSequenceDisplay/model.js

@@ -1,8 +1,8 @@
 import { addDisposer, types } from 'mobx-state-tree';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
-import { ConfigurationReference, } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
-import { getContainingView } from '@jbrowse/core/util';
+import { getContainingTrack, getContainingView } from '@jbrowse/core/util';
 import { autorun } from 'mobx';
 /**
  * #stateModel LinearReferenceSequenceDisplay
@@ -37,18 +37,47 @@ export function modelFactory(configSchema) {
          * #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 { showTranslation, showReverse, showForward } = self;
-            const r1 = showReverse && showTranslation ? self.rowHeight * 3 : 0;
-            const r2 = showForward && showTranslation ? self.rowHeight * 3 : 0;
+            const { rowHeight, showTranslationActual, showReverseActual, showForwardActual, } = self;
+            const r1 = showReverseActual && showTranslationActual ? rowHeight * 3 : 0;
+            const r2 = showForwardActual && showTranslationActual ? rowHeight * 3 : 0;
             const t = r1 + r2;
-            const r = showReverse ? self.rowHeight : 0;
-            const s = showForward ? self.rowHeight : 0;
+            const r = showReverseActual ? rowHeight : 0;
+            const s = showForwardActual ? rowHeight : 0;
             return t + r + s;
         },
     }))
@@ -59,15 +88,16 @@ export function modelFactory(configSchema) {
              * #method
              */
             renderProps() {
-                const { showForward, rpcDriverName, showReverse, showTranslation, rowHeight, sequenceHeight, } = self;
+                const { rpcDriverName, showForwardActual, showReverseActual, showTranslationActual, rowHeight, sequenceHeight, sequenceType, } = self;
                 return {
                     ...superRenderProps(),
                     ...getParentRenderProps(self),
                     config: self.configuration.renderer,
                     rpcDriverName,
-                    showForward,
-                    showReverse,
-                    showTranslation,
+                    showForward: showForwardActual,
+                    showReverse: showReverseActual,
+                    showTranslation: showTranslationActual,
+                    sequenceType,
                     rowHeight,
                     sequenceHeight,
                 };
@@ -80,7 +110,7 @@ export function modelFactory(configSchema) {
          */
         regionCannotBeRendered( /* region */) {
             const view = getContainingView(self);
-            return (view === null || view === void 0 ? void 0 : view.bpPerPx) > 3 ? 'Zoom in to see sequence' : undefined;
+            return view.bpPerPx > 3 ? 'Zoom in to see sequence' : undefined;
         },
         /**
          * #getter
@@ -111,7 +141,7 @@ export function modelFactory(configSchema) {
         afterAttach() {
             addDisposer(self, autorun(() => {
                 const view = getContainingView(self);
-                if ((view === null || view === void 0 ? void 0 : view.bpPerPx) > 3) {
+                if (view.bpPerPx > 3) {
                     self.setHeight(50);
                 }
                 else {
@@ -126,24 +156,34 @@ export function modelFactory(configSchema) {
          */
         trackMenuItems() {
             return [
-                {
-                    label: 'Show forward',
-                    type: 'checkbox',
-                    checked: self.showForward,
-                    onClick: () => self.toggleShowForward(),
-                },
-                {
-                    label: 'Show reverse',
-                    type: 'checkbox',
-                    checked: self.showReverse,
-                    onClick: () => self.toggleShowReverse(),
-                },
-                {
-                    label: 'Show translation',
-                    type: 'checkbox',
-                    checked: self.showTranslation,
-                    onClick: () => self.toggleShowTranslation(),
-                },
+                ...(self.sequenceType === 'dna'
+                    ? [
+                        {
+                            label: 'Show forward',
+                            type: 'checkbox',
+                            checked: self.showForward,
+                            onClick: () => {
+                                self.toggleShowForward();
+                            },
+                        },
+                        {
+                            label: 'Show reverse',
+                            type: 'checkbox',
+                            checked: self.showReverse,
+                            onClick: () => {
+                                self.toggleShowReverse();
+                            },
+                        },
+                        {
+                            label: 'Show translation',
+                            type: 'checkbox',
+                            checked: self.showTranslation,
+                            onClick: () => {
+                                self.toggleShowTranslation();
+                            },
+                        },
+                    ]
+                    : []),
             ];
         },
     }));

package/esm/ReferenceSequenceTrack/configSchema.d.ts

@@ -18,6 +18,22 @@ export declare function createReferenceSeqTrackConfig(pluginManager: PluginManag
         description: string;
         defaultValue: string;
     };
+    /**
+     * #slot
+     */
+    sequenceType: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
     /**
      * #slot
      */

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 // Note: this is primarily a copy of createBaseTrackConfig, except with a
@@ -29,6 +28,22 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             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
          */
@@ -66,7 +81,7 @@ export function createReferenceSeqTrackConfig(pluginManager) {
                 // snapshot
                 displays.forEach((d) => d && displayTypes.add(d.type));
                 const trackType = pluginManager.getTrackType(snap.type);
-                trackType.displayTypes.forEach(displayType => {
+                trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes.forEach(displayType => {
                     if (!displayTypes.has(displayType.name)) {
                         displays.push({
                             displayId: `${snap.trackId}-${displayType.name}`,

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -38,7 +38,7 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
             const searchForward = this.getConf('searchForward');
             const searchReverse = this.getConf('searchReverse');
             const caseInsensitive = this.getConf('caseInsensitive');
-            const re = new RegExp(search, 'g' + (caseInsensitive ? 'i' : ''));
+            const re = new RegExp(search, `g${caseInsensitive ? 'i' : ''}`);
             if (search) {
                 if (searchForward) {
                     const matches = residues.matchAll(re);

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -13,7 +13,10 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
         if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
             const file = openLocation(conf, this.pluginManager);
             const data = await file.readFile('utf8');
-            return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split(/\n|\r\n|\r/).filter(line => !!line.trim()).map(line => {
+            return Object.fromEntries(data
+                .split(/\n|\r\n|\r/)
+                .filter(line => !!line.trim())
+                .map(line => {
                 const [name, length] = line.split('\t');
                 return [name, +length];
             }));

package/esm/UnindexedFastaAdapter/UnindexedFastaAdapter.d.ts

@@ -0,0 +1,31 @@
+import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
+declare function parseSmallFasta(text: string): Map<string, {
+    readonly description: string;
+    readonly sequence: string;
+}>;
+export default class UnindexedFastaAdapter extends BaseSequenceAdapter {
+    protected setupP?: Promise<{
+        fasta: ReturnType<typeof parseSmallFasta>;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getRegions(opts?: BaseOptions): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    setupPre(_opts?: BaseOptions): Promise<{
+        fasta: Map<any, {
+            readonly description: string;
+            readonly sequence: string;
+        }>;
+    }>;
+    getHeader(): Promise<string | null>;
+    setup(opts?: BaseOptions): Promise<{
+        fasta: ReturnType<typeof parseSmallFasta>;
+    }>;
+    getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/esm/UnindexedFastaAdapter/UnindexedFastaAdapter.js

@@ -0,0 +1,84 @@
+import { BaseSequenceAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { readConfObject } from '@jbrowse/core/configuration';
+function parseSmallFasta(text) {
+    return new Map(text
+        .split('>')
+        .filter(t => /\S/.test(t))
+        .map(entryText => {
+        const [defLine, ...seqLines] = entryText.split('\n');
+        const [id, ...description] = defLine.split(' ');
+        const sequence = seqLines.join('').replace(/\s/g, '');
+        return [
+            id,
+            {
+                description: description.join(' '),
+                sequence,
+            },
+        ];
+    }));
+}
+export default class UnindexedFastaAdapter extends BaseSequenceAdapter {
+    async getRefNames(opts) {
+        const { fasta } = await this.setup(opts);
+        return [...fasta.keys()];
+    }
+    async getRegions(opts) {
+        const { fasta } = await this.setup(opts);
+        return [...fasta.entries()].map(([refName, data]) => ({
+            refName,
+            start: 0,
+            end: data.sequence.length,
+        }));
+    }
+    async setupPre(_opts) {
+        const fastaLocation = this.getConf('fastaLocation');
+        const res = parseSmallFasta(await openLocation(fastaLocation, this.pluginManager).readFile('utf8'));
+        return {
+            fasta: new Map([...res.entries()].map(([refName, val]) => {
+                return [
+                    readConfObject(this.config, 'rewriteRefNames', { refName }) ||
+                        refName,
+                    val,
+                ];
+            })),
+        };
+    }
+    async getHeader() {
+        const loc = this.getConf('metadataLocation');
+        return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
+            ? null
+            : openLocation(loc, this.pluginManager).readFile('utf8');
+    }
+    async setup(opts) {
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    getFeatures(region, opts) {
+        const { refName, start, end } = region;
+        return ObservableCreate(async (observer) => {
+            const { fasta } = await this.setup(opts);
+            const entry = fasta.get(refName);
+            if (entry) {
+                observer.next(new SimpleFeature({
+                    id: `${refName}-${start}-${end}`,
+                    data: {
+                        refName,
+                        start,
+                        end,
+                        seq: entry.sequence.slice(start, end),
+                    },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    freeResources( /* { region } */) { }
+}

package/esm/UnindexedFastaAdapter/configSchema.d.ts

@@ -0,0 +1,29 @@
+declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rewriteRefNames: {
+        type: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: string;
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default UnindexedFastaAdapter;

package/esm/UnindexedFastaAdapter/configSchema.js

@@ -0,0 +1,34 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config UnindexedFastaAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const UnindexedFastaAdapter = ConfigurationSchema('UnindexedFastaAdapter', {
+    rewriteRefNames: {
+        type: 'string',
+        defaultValue: '',
+        contextVariable: ['refName'],
+    },
+    /**
+     * #slot
+     */
+    fastaLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/seq.fa',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    metadataLocation: {
+        description: 'Optional metadata file',
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/fa.metadata.yaml',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+export default UnindexedFastaAdapter;

package/esm/UnindexedFastaAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function UnindexedFastaAdapterF(pluginManager: PluginManager): void;

package/esm/UnindexedFastaAdapter/index.js

@@ -0,0 +1,13 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function UnindexedFastaAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'UnindexedFastaAdapter',
+        displayName: 'Unindexed FASTA adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./UnindexedFastaAdapter').then(r => r.default),
+    }));
+}