@jbrowse/plugin-sequence 2.18.0 → 3.0.0

package/dist/BgzipFastaAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/ChromSizesAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

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

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature, Region } from '@jbrowse/core/util';
 import type { Theme } from '@mui/material';
@@ -17,5 +16,5 @@ declare const DivSequenceRendering: (props: {
     showForward?: boolean;
     showReverse?: boolean;
     showTranslation?: boolean;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DivSequenceRendering;

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,9 +1,7 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
@@ -34,24 +32,20 @@ function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqS
     const defaultFill = colorByCDS
         ? (_a = theme === null || theme === void 0 ? void 0 : theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a.main
         : (_b = theme === null || theme === void 0 ? void 0 : theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b.main;
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("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 = util_1.defaultStarts.includes(codon)
-                ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
-                : util_1.defaultStops.includes(codon)
-                    ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
-                    : undefined;
-            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, 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));
-        })));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.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 = util_1.defaultStarts.includes(codon)
+                    ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
+                    : util_1.defaultStops.includes(codon)
+                        ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
+                        : undefined;
+                return !(renderLetter || codonFill) ? null : ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: renderLetter
+                                ? codonWidth
+                                : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }), renderLetter ? ((0, jsx_runtime_1.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, theme, height, seq, y, }) {
     const render = 1 / bpPerPx >= 12;
@@ -61,16 +55,14 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
     const reverse = region.reversed;
     const len = e - s;
     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'
-            ?
-                theme.palette.bases[letter.toUpperCase()]
-            : undefined;
-        const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-        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));
-    })));
+    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: seq.split('').map((letter, index) => {
+            const color = sequenceType === 'dna'
+                ?
+                    theme.palette.bases[letter.toUpperCase()]
+                : undefined;
+            const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
+            return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }), render ? ((0, jsx_runtime_1.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, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
     const region = regions[0];
@@ -91,25 +83,20 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
     const [topFrames, bottomFrames] = region.reversed
         ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
         : [forwardFrames, reverseFrames];
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        topFrames.map(index => (react_1.default.createElement(Translation, { key: `translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }))),
-        showForward && showSequence ? (react_1.default.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
-        showReverse && showSequence ? (react_1.default.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
-        bottomFrames.map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${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 })))));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [topFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { 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 }, `translation-${index}`))), showForward && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null, showReverse && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null, bottomFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
-    return exportSVG ? (children) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
+    return exportSVG ? (children) : ((0, jsx_runtime_1.jsx)("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
             display: 'block',
             width,
             height: totalHeight,
             userSelect: 'none',
-        } }, children));
+        }, children: children }));
 }
 const DivSequenceRendering = (0, mobx_react_1.observer)(function (props) {
     const { regions, bpPerPx, sequenceHeight } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
-    return (react_1.default.createElement(Wrapper, { ...props, totalHeight: sequenceHeight, width: width },
-        react_1.default.createElement(SequenceSVG, { ...props })));
+    return ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, totalHeight: sequenceHeight, width: width, children: (0, jsx_runtime_1.jsx)(SequenceSVG, { ...props }) }));
 });
 exports.default = DivSequenceRendering;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -67,7 +67,7 @@ class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
             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 regionEnd = Math.min(size || 0, end);
                 const chunks = [];
                 const chunkSize = 128000;
                 const s = start - (start % chunkSize);

package/dist/IndexedFastaAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -34,7 +34,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -172,13 +172,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -205,7 +205,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     rowHeight: number;
@@ -270,7 +270,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/SequenceSearchAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/TwoBitAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/UnindexedFastaAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

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

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature, Region } from '@jbrowse/core/util';
 import type { Theme } from '@mui/material';
@@ -17,5 +16,5 @@ declare const DivSequenceRendering: (props: {
     showForward?: boolean;
     showReverse?: boolean;
     showTranslation?: boolean;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DivSequenceRendering;

package/esm/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,4 +1,5 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { Fragment } 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';
@@ -29,24 +30,20 @@ function Translation({ codonTable, seq, frame, bpPerPx, colorByCDS, region, seqS
     const defaultFill = colorByCDS
         ? (_a = theme === null || theme === void 0 ? void 0 : theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a.main
         : (_b = theme === null || theme === void 0 ? void 0 : theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b.main;
-    return (React.createElement(React.Fragment, null,
-        React.createElement("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 === null || theme === void 0 ? void 0 : theme.palette.startCodon
-                : defaultStops.includes(codon)
-                    ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
-                    : undefined;
-            return !(renderLetter || codonFill) ? null : (React.createElement(React.Fragment, { key: `${index}-${letter}` },
-                React.createElement("rect", { x: x, y: y, width: renderLetter
-                        ? codonWidth
-                        : 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));
-        })));
+    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 === null || theme === void 0 ? void 0 : theme.palette.startCodon
+                    : defaultStops.includes(codon)
+                        ? theme === null || theme === void 0 ? void 0 : 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, theme, height, seq, y, }) {
     const render = 1 / bpPerPx >= 12;
@@ -56,16 +53,14 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
     const reverse = region.reversed;
     const len = e - s;
     const w = Math.max((rightPx - leftPx) / len, 0.8);
-    return (React.createElement(React.Fragment, null, seq.split('').map((letter, index) => {
-        const color = sequenceType === 'dna'
-            ?
-                theme.palette.bases[letter.toUpperCase()]
-            : undefined;
-        const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-        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));
-    })));
+    return (_jsx(_Fragment, { children: seq.split('').map((letter, index) => {
+            const color = sequenceType === 'dna'
+                ?
+                    theme.palette.bases[letter.toUpperCase()]
+                : undefined;
+            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 ? 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, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
     const region = regions[0];
@@ -86,25 +81,20 @@ function SequenceSVG({ regions, theme: configTheme, colorByCDS, features = new M
     const [topFrames, bottomFrames] = region.reversed
         ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
         : [forwardFrames, reverseFrames];
-    return (React.createElement(React.Fragment, null,
-        topFrames.map(index => (React.createElement(Translation, { key: `translation-${index}`, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }))),
-        showForward && showSequence ? (React.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
-        showReverse && showSequence ? (React.createElement(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
-        bottomFrames.map(index => (React.createElement(Translation, { key: `rev-translation-${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 })))));
+    return (_jsxs(_Fragment, { children: [topFrames.map(index => (_jsx(Translation, { 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 }, `translation-${index}`))), showForward && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null, showReverse && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null, bottomFrames.map(index => (_jsx(Translation, { colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
 }
 function Wrapper({ exportSVG, width, totalHeight, children, }) {
-    return exportSVG ? (children) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
+    return exportSVG ? (children) : (_jsx("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
             display: 'block',
             width,
             height: totalHeight,
             userSelect: 'none',
-        } }, children));
+        }, children: children }));
 }
 const DivSequenceRendering = observer(function (props) {
     const { regions, bpPerPx, sequenceHeight } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
-    return (React.createElement(Wrapper, { ...props, totalHeight: sequenceHeight, width: width },
-        React.createElement(SequenceSVG, { ...props })));
+    return (_jsx(Wrapper, { ...props, totalHeight: sequenceHeight, width: width, children: _jsx(SequenceSVG, { ...props }) }));
 });
 export default DivSequenceRendering;

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -62,7 +62,7 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
             await updateStatus2('Downloading sequence', statusCallback, stopToken, async () => {
                 const { fasta } = await this.setup();
                 const size = await fasta.getSequenceSize(refName);
-                const regionEnd = Math.min(size, end);
+                const regionEnd = Math.min(size || 0, end);
                 const chunks = [];
                 const chunkSize = 128000;
                 const s = start - (start % chunkSize);

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -34,7 +34,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -172,13 +172,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -205,7 +205,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     rowHeight: number;
@@ -270,7 +270,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,8 +37,8 @@
   },
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/indexedfasta": "^2.0.2",
-    "@gmod/twobit": "^3.0.1"
+    "@gmod/indexedfasta": "^3.0.0",
+    "@gmod/twobit": "^4.0.1"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -57,5 +57,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }