@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearSyntenyView/model.js

@@ -0,0 +1,170 @@
+"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 = require("react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const file_saver_1 = require("file-saver");
+// icons
+const CropFree_1 = __importDefault(require("@mui/icons-material/CropFree"));
+const Link_1 = __importDefault(require("@mui/icons-material/Link"));
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
+const Icons_1 = require("./components/Icons");
+// locals
+const model_1 = __importDefault(require("../LinearComparativeView/model"));
+// lazies
+const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
+/**
+ * #stateModel LinearSyntenyView
+ * extends the `LinearComparativeView` base model
+ */
+function stateModelFactory(pluginManager) {
+    return mobx_state_tree_1.types
+        .compose((0, model_1.default)(pluginManager), mobx_state_tree_1.types.model('LinearSyntenyView', {
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LinearSyntenyView'),
+        /**
+         * #property/
+         */
+        drawCIGAR: true,
+        /**
+         * #property
+         */
+        drawCurves: false,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        toggleCurves() {
+            self.drawCurves = !self.drawCurves;
+        },
+        /**
+         * #action
+         */
+        toggleCIGAR() {
+            self.drawCIGAR = !self.drawCIGAR;
+        },
+        /**
+         * #action
+         */
+        showAllRegions() {
+            (0, mobx_1.transaction)(() => {
+                self.views.forEach(view => view.showAllRegionsInAssembly());
+            });
+        },
+    }))
+        .actions(self => ({
+        async exportSvg(opts) {
+            const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGLinearSyntenyView')));
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
+        },
+    }))
+        .views(self => {
+        const superHeaderMenuItems = self.headerMenuItems;
+        const superMenuItems = self.menuItems;
+        return {
+            /**
+             * #method
+             * includes a subset of view menu options because the full list is a
+             * little overwhelming
+             */
+            headerMenuItems() {
+                return [
+                    ...superHeaderMenuItems(),
+                    {
+                        label: 'Square view',
+                        onClick: self.squareView,
+                        description: 'Makes both views use the same zoom level, adjusting to the average of each',
+                        icon: CropFree_1.default,
+                    },
+                    {
+                        label: 'Show all regions',
+                        onClick: self.showAllRegions,
+                        description: 'Show entire genome assemblies',
+                        icon: Visibility_1.default,
+                    },
+                    {
+                        label: 'Draw CIGAR',
+                        onClick: self.toggleCIGAR,
+                        checked: self.drawCIGAR,
+                        type: 'checkbox',
+                        description: 'Draws per-base CIGAR level alignments',
+                    },
+                    {
+                        label: 'Link views',
+                        type: 'checkbox',
+                        checked: self.linkViews,
+                        onClick: self.toggleLinkViews,
+                        icon: Link_1.default,
+                    },
+                    {
+                        label: 'Use curved lines',
+                        type: 'checkbox',
+                        checked: self.drawCurves,
+                        onClick: self.toggleCurves,
+                        icon: Icons_1.Curves,
+                    },
+                    {
+                        label: 'Export SVG',
+                        icon: PhotoCamera_1.default,
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                ExportSvgDialog,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                ];
+            },
+            menuItems() {
+                return [
+                    ...superMenuItems(),
+                    {
+                        label: 'Export SVG',
+                        icon: PhotoCamera_1.default,
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                ExportSvgDialog,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                ];
+            },
+        };
+    });
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LinearSyntenyView/model.js.map

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package/dist/LinearSyntenyView/svgcomponents/SVGBackground.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): React.JSX.Element;

package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -0,0 +1,13 @@
+"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 material_1 = require("@mui/material");
+function SVGBackground({ width, height, shift, }) {
+    const theme = (0, material_1.useTheme)();
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+exports.default = SVGBackground;
+//# sourceMappingURL=SVGBackground.js.map

package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js.map

@@ -0,0 +1 @@
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package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts

@@ -0,0 +1,4 @@
+import { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+type LSV = LinearSyntenyViewModel;
+export declare function renderToSvg(model: LSV, opts: ExportSvgOptions): Promise<string>;
+export {};

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -0,0 +1,85 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderToSvg = void 0;
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const server_1 = require("react-dom/server");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const ui_1 = require("@jbrowse/core/ui");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+// locals
+const SVGBackground_1 = __importDefault(require("./SVGBackground"));
+const drawSynteny_1 = require("../../LinearSyntenyDisplay/drawSynteny");
+// render LGV to SVG
+async function renderToSvg(model, opts) {
+    var _a;
+    await (0, mobx_1.when)(() => model.initialized);
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), themeName = 'default', } = opts;
+    const session = (0, util_1.getSession)(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, views, middleComparativeHeight: synH, tracks } = model;
+    const shift = 50;
+    const offset = headerHeight + rulerHeight;
+    const heights = views.map(v => (0, plugin_linear_genome_view_1.totalHeight)(v.tracks, textHeight, trackLabels) + offset);
+    const totalHeightSvg = (0, util_1.sum)(heights) + synH + 100;
+    const displayResults = await Promise.all(views.map(async (view) => ({
+        view,
+        data: await Promise.all(view.tracks.map(async (track) => {
+            const d = track.displays[0];
+            await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
+            return { track, result: await d.renderSvg({ ...opts, theme }) };
+        })),
+    })));
+    const renderings = await Promise.all(tracks.map(async (track) => {
+        const d = track.displays[0];
+        await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
+        const r = await (0, util_1.renderToAbstractCanvas)(width, synH, { exportSVG: opts }, ctx => (0, drawSynteny_1.drawRef)(d, ctx));
+        if ('imageData' in r) {
+            throw new Error('found a canvas in svg export, probably a bug');
+        }
+        else if ('canvasRecordedData' in r) {
+            return {
+                html: await (0, util_1.getSerializedSvg)({
+                    ...r,
+                    width,
+                    height: synH,
+                }),
+            };
+        }
+        else {
+            return r;
+        }
+    }));
+    const trackLabelMaxLen = (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0) + 40;
+    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
+    const w = width + trackLabelOffset;
+    const t = (0, ui_1.createJBrowseTheme)(theme);
+    // the xlink namespace is used for rendering <image> tag
+    return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
+        react_1.default.createElement(Wrapper, null,
+            react_1.default.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
+                react_1.default.createElement(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }),
+                react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },
+                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
+                    react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                react_1.default.createElement("defs", null,
+                    react_1.default.createElement("clipPath", { id: 'synclip' },
+                        react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: synH }))),
+                react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
+                react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
+                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
+                    react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))));
+}
+exports.renderToSvg = renderToSvg;
+//# sourceMappingURL=SVGLinearSyntenyView.js.map

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js.map

@@ -0,0 +1 @@
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package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
+    model: any;
+}) => React.JSX.Element;
+export default BreakpointAlignmentsFeatureDetail;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -0,0 +1,66 @@
+"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 copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+function Formatter({ value }) {
+    const [show, setShow] = (0, react_1.useState)(false);
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const display = String(value);
+    if (display.length > 100) {
+        return (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement("button", { type: "button", onClick: () => {
+                    (0, copy_to_clipboard_1.default)(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                } }, copied ? 'Copied to clipboard' : 'Copy'),
+            react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
+    }
+    return react_1.default.createElement("div", null, display);
+}
+function CustomFeatureDetails(props) {
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseAttributes, { ...props, formatter: (value) => react_1.default.createElement(Formatter, { value: value }) }));
+}
+const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ model }) => {
+    const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
+    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
+        react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
+        react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
+        react_1.default.createElement(CustomFeatureDetails, { feature: feature1 }),
+        react_1.default.createElement(CustomFeatureDetails, { feature: feature2 })));
+});
+exports.default = BreakpointAlignmentsFeatureDetail;
+//# sourceMappingURL=SyntenyFeatureDetail.js.map

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SyntenyFeatureDetail.js","sourceRoot":"","sources":["../../src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,0EAAoC;AACpC,4CAAqC;AACrC,2CAAqC;AACrC,yFAG0D;AAG1D,SAAS,SAAS,CAAC,EAAE,KAAK,EAAsB;IAC9C,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,OAAO,CAAC,MAAM,GAAG,GAAG,EAAE;QACxB,OAAO,CACL;YACE,0CACE,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAA,2BAAI,EAAC,OAAO,CAAC,CAAA;oBACb,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,UAAU,CAAC,GAAG,EAAE;wBACd,SAAS,CAAC,KAAK,CAAC,CAAA;oBAClB,CAAC,EAAE,GAAG,CAAC,CAAA;gBACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CACjC;YACT,0CAAQ,IAAI,EAAC,QAAQ,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IACtD,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAC1B;YACT,2CAAM,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAO,CAC1D,CACJ,CAAA;KACF;IACD,OAAO,2CAAM,OAAO,CAAO,CAAA;AAC7B,CAAC;AAED,SAAS,oBAAoB,CAAC,KAA2C;IACvE,OAAO,CACL,8BAAC,kCAAc,OACT,KAAK,EACT,SAAS,EAAE,CAAC,KAAc,EAAE,EAAE,CAAC,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,GAC1D,CACH,CAAA;AACH,CAAC;AAED,MAAM,iCAAiC,GAAG,IAAA,qBAAQ;AAChD,8DAA8D;AAC9D,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC5B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAA;IAC5E,OAAO,CACL,8BAAC,gBAAK,mBAAa,uBAAuB;QACxC,8BAAC,mCAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,8BAAC,mCAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,8BAAC,oBAAoB,IAAC,OAAO,EAAE,QAAQ,GAAI;QAC3C,8BAAC,oBAAoB,IAAC,OAAO,EAAE,QAAQ,GAAI,CACrC,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,iCAAiC,CAAA"}

package/dist/SyntenyFeatureDetail/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/SyntenyFeatureDetail/index.js

@@ -0,0 +1,58 @@
+"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 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configSchema = (0, configuration_1.ConfigurationSchema)('SyntenyFeatureWidget', {});
+const stateModel = mobx_state_tree_1.types
+    .model('SyntenyFeatureWidget', {
+    id: mst_1.ElementId,
+    type: mobx_state_tree_1.types.literal('SyntenyFeatureWidget'),
+    featureData: mobx_state_tree_1.types.frozen(),
+})
+    .actions(self => ({
+    setFeatureData(data) {
+        self.featureData = data;
+    },
+    clearFeatureData() {
+        self.featureData = undefined;
+    },
+}));
+exports.default = (pluginManager) => {
+    pluginManager.addWidgetType(() => new WidgetType_1.default({
+        name: 'SyntenyFeatureWidget',
+        heading: 'Synteny feature details',
+        configSchema,
+        stateModel,
+        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SyntenyFeatureDetail')))),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/dist/SyntenyFeatureDetail/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SyntenyFeatureDetail/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAC5B,+DAAiE;AACjE,gGAAuE;AAEvE,sDAAwD;AACxD,qDAAuC;AAEvC,MAAM,YAAY,GAAG,IAAA,mCAAmB,EAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAEpE,MAAM,UAAU,GAAG,uBAAK;KACrB,KAAK,CAAC,sBAAsB,EAAE;IAC7B,EAAE,EAAE,eAAS;IACb,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;IAC3C,WAAW,EAAE,uBAAK,CAAC,MAAM,EAAE;CAC5B,CAAC;KACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,cAAc,CAAC,IAAa;QAC1B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAA;IACzB,CAAC;IACD,gBAAgB;QACd,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;IAC9B,CAAC;CACF,CAAC,CAAC,CAAA;AAEL,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,aAAa,CACzB,GAAG,EAAE,CACH,IAAI,oBAAU,CAAC;QACb,IAAI,EAAE,sBAAsB;QAC5B,OAAO,EAAE,yBAAyB;QAClC,YAAY;QACZ,UAAU;QACV,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,wBAAwB,GAAC,CAAC;KAC7D,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/SyntenyTrack/configSchema.d.ts

@@ -0,0 +1,75 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+export default configSchema;

package/dist/SyntenyTrack/configSchema.js

@@ -0,0 +1,16 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+/**
+ * #config SyntenyTrack
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SyntenyTrack', {}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
+});
+exports.default = configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/SyntenyTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SyntenyTrack/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,uEAAkF;AAGlF;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,IAAA,mCAAmB,EACjB,cAAc,EACd,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;CACxD,CACF,CAAA;AAEH,kBAAe,YAAY,CAAA"}

package/dist/SyntenyTrack/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pm: PluginManager) => void;
+export default _default;

package/dist/SyntenyTrack/index.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 });
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = (0, configSchema_1.default)(pm);
+        return new TrackType_1.default({
+            name: 'SyntenyTrack',
+            configSchema,
+            stateModel: (0, models_1.createBaseTrackModel)(pm, 'SyntenyTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/SyntenyTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SyntenyTrack/index.tsx"],"names":[],"mappings":";;;;;AAAA,uEAAiF;AACjF,8FAAqE;AAErE,kEAA0C;AAE1C,kBAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/index.d.ts

@@ -0,0 +1,7 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,47 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const util_1 = require("@jbrowse/core/util");
+const CalendarViewDay_1 = __importDefault(require("@mui/icons-material/CalendarViewDay"));
+const LinearComparativeDisplay_1 = __importDefault(require("./LinearComparativeDisplay"));
+const LinearComparativeView_1 = __importDefault(require("./LinearComparativeView"));
+const LinearSyntenyDisplay_1 = __importDefault(require("./LinearSyntenyDisplay"));
+const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
+const LinearSyntenyView_1 = __importDefault(require("./LinearSyntenyView"));
+const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
+const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
+const SyntenyFeatureDetail_1 = __importDefault(require("./SyntenyFeatureDetail"));
+const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
+class default_1 extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'LinearComparativeViewPlugin';
+    }
+    install(pluginManager) {
+        (0, LinearComparativeView_1.default)(pluginManager);
+        (0, LinearSyntenyView_1.default)(pluginManager);
+        (0, LinearComparativeDisplay_1.default)(pluginManager);
+        (0, LinearSyntenyDisplay_1.default)(pluginManager);
+        (0, LGVSyntenyDisplay_1.default)(pluginManager);
+        (0, LaunchLinearSyntenyView_1.default)(pluginManager);
+        (0, SyntenyTrack_1.default)(pluginManager);
+        (0, SyntenyFeatureDetail_1.default)(pluginManager);
+        (0, LinearReadVsRef_1.default)(pluginManager);
+    }
+    configure(pluginManager) {
+        if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {
+            pluginManager.rootModel.appendToSubMenu(['Add'], {
+                label: 'Linear synteny view',
+                icon: CalendarViewDay_1.default,
+                onClick: (session) => {
+                    session.addView('LinearSyntenyView', {});
+                },
+            });
+        }
+    }
+}
+exports.default = default_1;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.tsx"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAEzC,6CAAgF;AAEhF,0FAA8D;AAC9D,0FAAkE;AAClE,oFAA4D;AAC5D,kFAA0D;AAC1D,4EAAoD;AACpD,4EAAoD;AACpD,wFAAgE;AAChE,kEAA0C;AAC1C,kFAA0D;AAC1D,wEAAuD;AAEvD,eAAqB,SAAQ,gBAAM;IAAnC;;QACE,SAAI,GAAG,6BAA6B,CAAA;IAyBtC,CAAC;IAvBC,OAAO,CAAC,aAA4B;QAClC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,kCAAyB,EAAC,aAAa,CAAC,CAAA;QACxC,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,iCAAwB,EAAC,aAAa,CAAC,CAAA;QACvC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,8BAAqB,EAAC,aAAa,CAAC,CAAA;QACpC,IAAA,yBAAuB,EAAC,aAAa,CAAC,CAAA;IACxC,CAAC;IAED,SAAS,CAAC,aAA4B;QACpC,IAAI,IAAA,4BAAqB,EAAC,aAAa,CAAC,SAAS,CAAC,EAAE;YAClD,aAAa,CAAC,SAAS,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,KAAK,EAAE,qBAAqB;gBAC5B,IAAI,EAAE,yBAAY;gBAClB,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,OAAO,CAAC,OAAO,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAA;gBAC1C,CAAC;aACF,CAAC,CAAA;SACH;IACH,CAAC;CACF;AA1BD,4BA0BC"}