@jbrowse/plugin-sequence 3.6.5 → 4.0.0

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
-import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter.ts';
 export default class BgzipFastaAdapter extends IndexedFasta {
     setupPre(): Promise<{
         fasta: BgzipIndexedFasta;

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,6 +1,6 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import { openLocation } from '@jbrowse/core/util/io';
-import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+import IndexedFasta from "../IndexedFastaAdapter/IndexedFastaAdapter.js";
 export default class BgzipFastaAdapter extends IndexedFasta {
     async setupPre() {
         const fastaLocation = this.getConf('fastaLocation');

package/esm/BgzipFastaAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BgzipFastaAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -28,5 +28,5 @@ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurati
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BgzipFastaAdapter;

package/esm/BgzipFastaAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function BgzipFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -9,7 +9,7 @@ export default function BgzipFastaAdapterF(pluginManager) {
             adapterMetadata: {
                 hiddenFromGUI: true,
             },
-            getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
+            getAdapterClass: () => import("./BgzipFastaAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,6 +1,7 @@
 import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 export default class ChromSizesAdapter extends BaseAdapter {
+    setupP;
     async setupPre() {
         const pm = this.pluginManager;
         const file = openLocation(this.getConf('chromSizesLocation'), pm);

package/esm/ChromSizesAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const ChromSizesAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     chromSizesLocation: {
         type: string;
         defaultValue: {
@@ -6,5 +6,5 @@ declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurati
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default ChromSizesAdapter;

package/esm/ChromSizesAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function ChromSizesAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ChromSizesAdapter',
@@ -8,6 +8,6 @@ export default function ChromSizesAdapterF(pluginManager) {
         adapterMetadata: {
             hiddenFromGUI: true,
         },
-        getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
+        getAdapterClass: () => import("./ChromSizesAdapter.js").then(r => r.default),
     }));
 }

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,71 +1,9 @@
-import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
-import { Fragment } from 'react';
-import { bpSpanPx, complement, defaultCodonTable, defaultStarts, defaultStops, generateCodonTable, revcom, } from '@jbrowse/core/util';
-import { useTheme } from '@mui/material';
+import { jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
+import { complement, defaultCodonTable, generateCodonTable, } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, }) {
-    var _a, _b;
-    const normalizedFrame = Math.abs(frame) - 1;
-    const seqFrame = seqStart % 3;
-    const frameShift = (normalizedFrame - seqFrame + 3) % 3;
-    const theme = useTheme();
-    const frameShiftAdjustedSeqLength = seq.length - frameShift;
-    const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
-    const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
-    const translated = [];
-    for (let i = 0; i < seqSliced.length; i += 3) {
-        const codon = seqSliced.slice(i, i + 3);
-        const normalizedCodon = reverse ? revcom(codon) : codon;
-        const aminoAcid = codonTable[normalizedCodon] || '';
-        translated.push({
-            letter: aminoAcid,
-            codon: normalizedCodon.toUpperCase(),
-        });
-    }
-    const codonWidth = (1 / bpPerPx) * 3;
-    const renderLetter = 1 / bpPerPx >= 12;
-    const frameOffset = frameShift / bpPerPx;
-    const startOffset = (region.start - seqStart) / bpPerPx;
-    const offset = frameOffset - startOffset;
-    const dark = theme.palette.mode === 'dark' ? 'dark' : 'main';
-    const defaultFill = colorByCDS
-        ? (_a = theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a[dark]
-        : (_b = theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b[dark];
-    return (_jsxs(_Fragment, { children: [_jsx("rect", { x: 0, y: y, width: width, height: height, fill: defaultFill }), translated.map((element, index) => {
-                const x = region.reversed
-                    ? width - (index + 1) * codonWidth - offset
-                    : codonWidth * index + offset;
-                const { letter, codon } = element;
-                const codonFill = defaultStarts.includes(codon)
-                    ? theme.palette.startCodon
-                    : defaultStops.includes(codon)
-                        ? theme.palette.stopCodon
-                        : undefined;
-                return !(renderLetter || codonFill) ? null : (_jsxs(Fragment, { children: [_jsx("rect", { x: x, y: y, width: renderLetter
-                                ? codonWidth
-                                : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }), renderLetter ? (_jsx("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", children: letter })) : null] }, `${index}-${letter}`));
-            })] }));
-}
-function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }) {
-    const render = 1 / bpPerPx >= 12;
-    const s = feature.get('start');
-    const e = feature.get('end');
-    const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx);
-    const reverse = region.reversed;
-    const len = e - s;
-    const w = Math.max((rightPx - leftPx) / len, 0.8);
-    const theme = useTheme();
-    return (_jsx(_Fragment, { children: seq.split('').map((letter, index) => {
-            const color = sequenceType === 'dna'
-                ?
-                    theme.palette.bases[letter.toUpperCase()]
-                : undefined;
-            const dark = theme.palette.mode === 'dark';
-            const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-            return (_jsxs(Fragment, { children: [_jsx("rect", { x: x, y: y, width: w, height: height, fill: color ? (dark ? color.dark : color.main) : '#aaa', stroke: render ? '#555' : 'none' }), render ? (_jsx("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
-        }) }));
-}
-function SequenceSVG({ regions, width, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
+import Sequence from "./Sequence.js";
+import Translation from "./Translation.js";
+function SequenceSVG({ regions, width, colorByCDS, features, showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
     const region = regions[0];
     const codonTable = generateCodonTable(defaultCodonTable);
     const [feature] = [...features.values()];
@@ -76,14 +14,31 @@ function SequenceSVG({ regions, width, colorByCDS, features = new Map(), showRev
     if (!seq) {
         return null;
     }
-    let currY = -rowHeight;
     const showSequence = bpPerPx <= 1;
     const forwardFrames = showTranslation && showForward ? [3, 2, 1] : [];
     const reverseFrames = showTranslation && showReverse ? [-1, -2, -3] : [];
     const [topFrames, bottomFrames] = region.reversed
         ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
         : [forwardFrames, reverseFrames];
-    return (_jsxs(_Fragment, { children: [topFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx })) : null, showReverse && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx })) : null, bottomFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
+    const elements = [];
+    let currentY = 0;
+    for (const index of topFrames) {
+        elements.push(_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: currentY, codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: region.reversed }, `translation-${index}`));
+        currentY += rowHeight;
+    }
+    if (showForward && showSequence) {
+        elements.push(_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: currentY, feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx }, "forward_seq"));
+        currentY += rowHeight;
+    }
+    if (showReverse && showSequence) {
+        elements.push(_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: currentY, feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx }, "reverse_seq"));
+        currentY += rowHeight;
+    }
+    for (const index of bottomFrames) {
+        elements.push(_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: currentY, codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`));
+        currentY += rowHeight;
+    }
+    return _jsx(_Fragment, { children: elements });
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
     return exportSVG ? (children) : (_jsx("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
@@ -93,7 +48,7 @@ function Wrapper({ exportSVG, width, totalHeight, children, }) {
             userSelect: 'none',
         }, children: children }));
 }
-const DivSequenceRendering = observer(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }) {
+const DivSequenceRendering = observer(function DivSequenceRendering({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }) {
     const region = regions[0];
     const width = Math.ceil((region.end - region.start) / bpPerPx);
     return (_jsx(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: _jsx(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));

package/esm/DivSequenceRenderer/components/Sequence.d.ts

@@ -0,0 +1,10 @@
+import type { Feature, Region } from '@jbrowse/core/util';
+export default function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }: {
+    seq: string;
+    bpPerPx: number;
+    sequenceType: string;
+    height: number;
+    region: Region;
+    feature: Feature;
+    y: number;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/DivSequenceRenderer/components/Sequence.js

@@ -0,0 +1,32 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { bpSpanPx } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
+export default function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }) {
+    const theme = useTheme();
+    const render = 1 / bpPerPx >= 12;
+    const s = feature.get('start');
+    const e = feature.get('end');
+    const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx);
+    const reverse = region.reversed;
+    const len = e - s;
+    const w = Math.max((rightPx - leftPx) / len, 0.8);
+    let svg = '';
+    for (let i = 0, l = seq.length; i < l; i++) {
+        const letter = seq[i];
+        const color = sequenceType === 'dna'
+            ?
+                theme.palette.bases[letter.toUpperCase()]
+            : undefined;
+        const x = reverse ? rightPx - (i + 1) * w : leftPx + i * w;
+        const fill = color ? color.main : '#aaa';
+        const stroke = render ? '#555' : 'none';
+        svg += `<rect x="${x}" y="${y}" width="${w}" height="${height}" fill="${fill}" stroke="${stroke}"/>`;
+        if (render) {
+            const textFill = color
+                ? theme.palette.getContrastText(color.main)
+                : 'black';
+            svg += `<text x="${x + w / 2}" y="${y + height / 2}" dominant-baseline="middle" text-anchor="middle" font-size="${height - 2}" fill="${textFill}">${letter}</text>`;
+        }
+    }
+    return _jsx("g", { dangerouslySetInnerHTML: { __html: svg } });
+}

package/esm/DivSequenceRenderer/components/Translation.d.ts

@@ -0,0 +1,14 @@
+import type { Frame, Region } from '@jbrowse/core/util';
+export default function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse, }: {
+    codonTable: Record<string, string>;
+    width: number;
+    seq: string;
+    frame: Frame;
+    colorByCDS: boolean;
+    bpPerPx: number;
+    region: Region;
+    seqStart: number;
+    reverse?: boolean;
+    height: number;
+    y: number;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/DivSequenceRenderer/components/Translation.js

@@ -0,0 +1,54 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { defaultStarts, defaultStops, revcom } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
+export default function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, }) {
+    const theme = useTheme();
+    const normalizedFrame = Math.abs(frame) - 1;
+    const seqFrame = seqStart % 3;
+    const frameShift = (normalizedFrame - seqFrame + 3) % 3;
+    const frameShiftAdjustedSeqLength = seq.length - frameShift;
+    const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
+    const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
+    const translated = [];
+    for (let i = 0; i < seqSliced.length; i += 3) {
+        const codon = seqSliced.slice(i, i + 3);
+        const normalizedCodon = reverse ? revcom(codon) : codon;
+        const aminoAcid = codonTable[normalizedCodon] || '';
+        translated.push({
+            letter: aminoAcid,
+            codon: normalizedCodon.toUpperCase(),
+        });
+    }
+    const codonWidth = (1 / bpPerPx) * 3;
+    const renderLetter = 1 / bpPerPx >= 12;
+    const frameOffset = frameShift / bpPerPx;
+    const startOffset = (region.start - seqStart) / bpPerPx;
+    const offset = frameOffset - startOffset;
+    const defaultFill = colorByCDS
+        ? theme.palette.framesCDS.at(frame)?.main
+        : theme.palette.frames.at(frame)?.main;
+    let svg = `<rect x="0" y="${y}" width="${width}" height="${height}" fill="${defaultFill}"/>`;
+    for (let i = 0, l = translated.length; i < l; i++) {
+        const element = translated[i];
+        const x = region.reversed
+            ? width - (i + 1) * codonWidth - offset
+            : codonWidth * i + offset;
+        const { letter, codon } = element;
+        const codonFill = defaultStarts.includes(codon)
+            ? theme.palette.startCodon
+            : defaultStops.includes(codon)
+                ? theme.palette.stopCodon
+                : undefined;
+        if (renderLetter || codonFill) {
+            const rectWidth = renderLetter
+                ? codonWidth
+                : codonWidth + 0.7;
+            const stroke = renderLetter ? '#555' : 'none';
+            svg += `<rect x="${x}" y="${y}" width="${rectWidth}" height="${height}" stroke="${stroke}" fill="${codonFill || 'none'}"/>`;
+            if (renderLetter) {
+                svg += `<text x="${x + codonWidth / 2}" font-size="${height - 2}" y="${y + height / 2}" dominant-baseline="middle" text-anchor="middle">${letter}</text>`;
+            }
+        }
+    }
+    return _jsx("g", { dangerouslySetInnerHTML: { __html: svg } });
+}

package/esm/DivSequenceRenderer/configSchema.d.ts

@@ -1,8 +1,8 @@
-declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const DivSequenceRenderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     height: {
         type: string;
         description: string;
         defaultValue: number;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default DivSequenceRenderer;

package/esm/DivSequenceRenderer/index.js

@@ -1,23 +1,17 @@
+import { lazy } from 'react';
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import ReactComponent from './components/DivSequenceRendering';
-import configSchema from './configSchema';
+import { expandRegion } from '@jbrowse/core/pluggableElementTypes/renderers/util';
+import configSchema from "./configSchema.js";
 class DivSequenceRenderer extends FeatureRendererType {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
+    supportsSVG = true;
     getExpandedRegion(region) {
-        return {
-            ...region,
-            start: Math.max(region.start - 3, 0),
-            end: region.end + 3,
-        };
+        return expandRegion(region, 3);
     }
 }
 export default function DivSequenceRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DivSequenceRenderer({
         name: 'DivSequenceRenderer',
-        ReactComponent,
+        ReactComponent: lazy(() => import("./components/DivSequenceRendering.js")),
         configSchema,
         pluginManager,
     }));

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -7,16 +7,14 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 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) => {
-                const { refName, start, end, fasta } = args;
-                return fasta.getSequence(refName, start, end);
-            },
-        });
-    }
+    setupP;
+    seqCache = new AbortablePromiseCache({
+        cache: new QuickLRU({ maxSize: 200 }),
+        fill: async (args) => {
+            const { refName, start, end, fasta } = args;
+            return fasta.getSequence(refName, start, end);
+        },
+    });
     async getRefNames(_opts) {
         const { fasta } = await this.setup();
         return fasta.getSequenceNames();
@@ -63,31 +61,25 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
                 const { fasta } = await this.setup();
                 const size = await fasta.getSequenceSize(refName);
                 const regionEnd = Math.min(size || 0, end);
-                const chunks = [];
                 const chunkSize = 128000;
                 const s = start - (start % chunkSize);
                 const e = end + (chunkSize - (end % chunkSize));
+                const chunkPromises = [];
                 for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
                     const r = {
                         refName,
                         start: chunkStart,
                         end: chunkStart + chunkSize,
                     };
-                    checkStopToken(stopToken);
-                    const res = await this.seqCache.get(JSON.stringify(r), {
+                    chunkPromises.push(this.seqCache.get(`${refName}-${chunkStart}-${r.end}`, {
                         ...r,
                         fasta,
-                    });
-                    if (!res) {
-                        break;
-                    }
-                    chunks.push(res);
+                    }));
                 }
-                const seq = chunks
-                    .filter(f => !!f)
-                    .join('')
-                    .slice(start - s)
-                    .slice(0, end - start);
+                checkStopToken(stopToken);
+                const chunks = await Promise.all(chunkPromises);
+                const len = end - start;
+                const seq = chunks.join('').slice(start - s, start - s + len);
                 if (seq) {
                     observer.next(new SimpleFeature({
                         id: `${refName}-${start}-${regionEnd}`,

package/esm/IndexedFastaAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const IndexedFastaAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -21,5 +21,5 @@ declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default IndexedFastaAdapter;

package/esm/IndexedFastaAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function IndexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -9,7 +9,7 @@ export default function IndexedFastaAdapterF(pluginManager) {
             adapterMetadata: {
                 hiddenFromGUI: true,
             },
-            getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
+            getAdapterClass: () => import("./IndexedFastaAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -1,9 +1,9 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    renderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         height: {
             type: string;
             description: string;
             defaultValue: number;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import divSequenceRendererConfigSchema from '../DivSequenceRenderer/configSchema';
+import divSequenceRendererConfigSchema from "../DivSequenceRenderer/configSchema.js";
 function x() { }
 export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', {
     renderer: divSequenceRendererConfigSchema,

package/esm/LinearReferenceSequenceDisplay/index.js

@@ -1,7 +1,7 @@
 import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
-import { configSchema } from './configSchema';
-import { modelFactory } from './model';
+import { configSchema } from "./configSchema.js";
+import { modelFactory } from "./model.js";
 export default function LinearReferenceSequenceDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const stateModel = modelFactory(configSchema);