@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearSyntenyDisplay/model.js

@@ -0,0 +1,179 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : 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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
+// locals
+const stateModelFactory_1 = __importDefault(require("../LinearComparativeDisplay/stateModelFactory"));
+/**
+ * #stateModel LinearSyntenyDisplay
+ * extends `LinearComparativeDisplay` model
+ */
+function stateModelFactory(configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearSyntenyDisplay', (0, stateModelFactory_1.default)(configSchema), mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LinearSyntenyDisplay'),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+    }))
+        .volatile(() => ({
+        // canvas used for drawing visible screen
+        mainCanvas: null,
+        // canvas used for drawing click map with feature ids
+        // this renders a unique color per alignment, so that it can be re-traced
+        // after a feature click with getImageData at that pixel
+        clickMapCanvas: null,
+        // canvas used for drawing click map with cigar data
+        // this can show if you are mousing over a insertion/deletion. it is similar
+        // in purpose to the clickMapRef but was not feasible to pack this into the
+        // clickMapRef
+        cigarClickMapCanvas: null,
+        // canvas for drawing mouseover shading
+        // this is separate from the other code for speed: don't have to redraw
+        // entire canvas to do a feature's mouseover shading
+        mouseoverCanvas: null,
+        // assigned by reaction
+        featPositions: [],
+        // currently mouse'd over feature
+        mouseoverId: undefined,
+        // currently click'd over feature
+        clickId: undefined,
+        // currently mouseover'd CIGAR subfeature
+        cigarMouseoverId: -1,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setFeatPositions(arg) {
+            self.featPositions = arg;
+        },
+        /**
+         * #action
+         */
+        setMainCanvasRef(ref) {
+            self.mainCanvas = ref;
+        },
+        /**
+         * #action
+         */
+        setClickMapCanvasRef(ref) {
+            self.clickMapCanvas = ref;
+        },
+        /**
+         * #action
+         */
+        setCigarClickMapCanvasRef(ref) {
+            self.cigarClickMapCanvas = ref;
+        },
+        /**
+         * #action
+         */
+        setMouseoverCanvasRef(ref) {
+            self.mouseoverCanvas = ref;
+        },
+        /**
+         * #action
+         */
+        setMouseoverId(arg) {
+            self.mouseoverId = arg;
+        },
+        /**
+         * #action
+         */
+        setCigarMouseoverId(arg) {
+            self.cigarMouseoverId = arg;
+        },
+        /**
+         * #action
+         */
+        setClickId(arg) {
+            self.clickId = arg;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get adapterConfig() {
+            return {
+                name: self.parentTrack.configuration.adapter.type,
+                assemblyNames: (0, configuration_1.getConf)(self, 'assemblyNames'),
+                ...(0, configuration_1.getConf)(self.parentTrack, 'adapter'),
+            };
+        },
+        /**
+         * #getter
+         */
+        get trackIds() {
+            return (0, configuration_1.getConf)(self, 'trackIds');
+        },
+        /**
+         * #getter
+         */
+        get numFeats() {
+            return self.featPositions.length;
+        },
+        /**
+         * #getter
+         * used for synteny svg rendering
+         */
+        get ready() {
+            return this.numFeats > 0;
+        },
+        /**
+         * #getter
+         */
+        get featMap() {
+            return Object.fromEntries(self.featPositions.map(f => [f.f.id(), f]));
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;
+            (async () => {
+                try {
+                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('./afterAttach')));
+                    doAfterAttach(self);
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            })();
+        },
+    }));
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LinearSyntenyDisplay/model.js.map

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package/dist/LinearSyntenyView/components/ExportSvgDialog.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { ExportSvgOptions } from '../model';
+export default function ExportSvgDlg({ model, handleClose, }: {
+    model: {
+        exportSvg(opts: ExportSvgOptions): Promise<void>;
+    };
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -0,0 +1,86 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : 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;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+function LoadingMessage() {
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
+        react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
+}
+function useSvgLocal(key, val) {
+    return (0, util_1.useLocalStorage)('svg-' + key, val);
+}
+function ExportSvgDlg({ model, handleClose, }) {
+    const session = (0, util_1.getSession)(model);
+    const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
+    const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
+    const [loading, setLoading] = (0, react_1.useState)(false);
+    const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
+    const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
+    const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
+    const [error, setError] = (0, react_1.useState)();
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
+        react_1.default.createElement(material_1.DialogContent, null,
+            error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
+            react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            react_1.default.createElement("br", null),
+            react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => setTrackLabels(event.target.value) },
+                react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
+                react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
+                react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
+                react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
+            react_1.default.createElement("br", null),
+            session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            // @ts-expect-error
+            val.name || '(Unknown name)'))))) : null,
+            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
+                    setLoading(true);
+                    setError(undefined);
+                    try {
+                        await model.exportSvg({
+                            rasterizeLayers,
+                            filename,
+                            themeName,
+                            trackLabels,
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setError(e);
+                    }
+                    finally {
+                        setLoading(false);
+                    }
+                } }, "Submit"))));
+}
+exports.default = ExportSvgDlg;
+//# sourceMappingURL=ExportSvgDialog.js.map

package/dist/LinearSyntenyView/components/ExportSvgDialog.js.map

@@ -0,0 +1 @@
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package/dist/LinearSyntenyView/components/Icons.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+import { SvgIconProps } from '@mui/material';
+export declare function Curves(props: SvgIconProps): React.JSX.Element;
+export declare function StraightLines(props: SvgIconProps): React.JSX.Element;

package/dist/LinearSyntenyView/components/Icons.js

@@ -0,0 +1,19 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.StraightLines = exports.Curves = void 0;
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+function Curves(props) {
+    return (react_1.default.createElement(material_1.SvgIcon, { ...props },
+        react_1.default.createElement("path", { fill: "currentColor", d: "M16.5,21C13.5,21 12.31,16.76 11.05,12.28C10.14,9.04 9,5 7.5,5C4.11,5 4,11.93 4,12H2C2,11.63 2.06,3 7.5,3C10.5,3 11.71,7.25 12.97,11.74C13.83,14.8 15,19 16.5,19C19.94,19 20.03,12.07 20.03,12H22.03C22.03,12.37 21.97,21 16.5,21Z" })));
+}
+exports.Curves = Curves;
+function StraightLines(props) {
+    return (react_1.default.createElement(material_1.SvgIcon, { ...props },
+        react_1.default.createElement("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" })));
+}
+exports.StraightLines = StraightLines;
+//# sourceMappingURL=Icons.js.map

package/dist/LinearSyntenyView/components/Icons.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Icons.js","sourceRoot":"","sources":["../../../src/LinearSyntenyView/components/Icons.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,4CAAqD;AAErD,SAAgB,MAAM,CAAC,KAAmB;IACxC,OAAO,CACL,8BAAC,kBAAO,OAAK,KAAK;QAChB,wCACE,IAAI,EAAC,cAAc,EACnB,CAAC,EAAC,mOAAmO,GACrO,CACM,CACX,CAAA;AACH,CAAC;AATD,wBASC;AAED,SAAgB,aAAa,CAAC,KAAmB;IAC/C,OAAO,CACL,8BAAC,kBAAO,OAAK,KAAK;QAChB,wCACE,IAAI,EAAC,cAAc,EACnB,CAAC,EAAC,6DAA6D,GAC/D,CACM,CACX,CAAA;AACH,CAAC;AATD,sCASC"}

package/dist/LinearSyntenyView/components/ImportCustomTrack.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import { SnapshotIn } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+type Conf = SnapshotIn<AnyConfigurationModel>;
+declare const OpenTrack: ({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }: {
+    sessionTrackData: Conf;
+    assembly1: string;
+    assembly2: string;
+    setSessionTrackData: (arg: Conf) => void;
+}) => React.JSX.Element;
+export default OpenTrack;

package/dist/LinearSyntenyView/components/ImportCustomTrack.js

@@ -0,0 +1,180 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : 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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const path_1 = __importDefault(require("path"));
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+function getName(sessionTrackData) {
+    return sessionTrackData
+        ? // @ts-expect-error
+            sessionTrackData.uri ||
+                // @ts-expect-error
+                sessionTrackData.localPath ||
+                // @ts-expect-error
+                sessionTrackData.name
+        : undefined;
+}
+function stripGz(fileName) {
+    return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
+}
+function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Location, bed2Location, }) {
+    if (radioOption === '.paf') {
+        return {
+            type: 'PAFAdapter',
+            pafLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.out') {
+        return {
+            type: 'MashMapAdapter',
+            outLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.delta') {
+        return {
+            type: 'DeltaAdapter',
+            deltaLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.chain') {
+        return {
+            type: 'ChainAdapter',
+            chainLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.anchors') {
+        return {
+            type: 'MCScanAnchorsAdapter',
+            mcscanAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else if (radioOption === '.anchors.simple') {
+        return {
+            type: 'MCScanSimpleAnchorsAdapter',
+            mcscanSimpleAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else {
+        throw new Error('Unknown type');
+    }
+}
+const OpenTrack = (0, mobx_react_1.observer)(({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }) => {
+    const [bed2Location, setBed2Location] = (0, react_1.useState)();
+    const [bed1Location, setBed1Location] = (0, react_1.useState)();
+    const [fileLocation, setFileLocation] = (0, react_1.useState)();
+    const [value, setValue] = (0, react_1.useState)('');
+    const [error, setError] = (0, react_1.useState)();
+    const fileName = getName(fileLocation);
+    const radioOption = value || (fileName ? path_1.default.extname(stripGz(fileName)) : '');
+    (0, react_1.useEffect)(() => {
+        try {
+            if (fileLocation) {
+                const fn = fileName ? path_1.default.basename(fileName) : 'MyTrack';
+                const trackId = `${fn}-${Date.now()}`;
+                setError(undefined);
+                setSessionTrackData({
+                    trackId,
+                    name: fn,
+                    assemblyNames: [assembly2, assembly1],
+                    type: 'SyntenyTrack',
+                    adapter: getAdapter({
+                        radioOption,
+                        assembly1,
+                        assembly2,
+                        fileLocation,
+                        bed1Location,
+                        bed2Location,
+                    }),
+                });
+            }
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }, [
+        fileName,
+        assembly1,
+        assembly2,
+        bed1Location,
+        bed2Location,
+        fileLocation,
+        radioOption,
+        setSessionTrackData,
+    ]);
+    return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
+        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
+        react_1.default.createElement(material_1.Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
+        react_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => setValue(event.target.value) },
+            react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".paf", control: react_1.default.createElement(material_1.Radio, null), label: ".paf" })),
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".out", control: react_1.default.createElement(material_1.Radio, null), label: ".out" })),
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".delta", control: react_1.default.createElement(material_1.Radio, null), label: ".delta" })),
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".chain", control: react_1.default.createElement(material_1.Radio, null), label: ".chain" })),
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors" })),
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors.simple", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors.simple" })))),
+        react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
+            react_1.default.createElement(material_1.Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (react_1.default.createElement("div", null,
+                react_1.default.createElement("div", { style: { margin: 20 } },
+                    "Open the ",
+                    value,
+                    " and .bed files for both genome assemblies from the MCScan (Python version) pipeline",
+                    ' ',
+                    react_1.default.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
+                react_1.default.createElement("div", { style: { display: 'flex' } },
+                    react_1.default.createElement("div", null,
+                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) })),
+                    react_1.default.createElement("div", null,
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => setBed1Location(loc) })),
+                    react_1.default.createElement("div", null,
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
+});
+exports.default = OpenTrack;
+//# sourceMappingURL=ImportCustomTrack.js.map

package/dist/LinearSyntenyView/components/ImportCustomTrack.js.map

@@ -0,0 +1 @@
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package/dist/LinearSyntenyView/components/ImportForm.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearSyntenyViewModel;
+}) => React.JSX.Element;
+export default _default;