@jbrowse/plugin-dotplot-view 2.6.1

package/dist/DotplotView/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, }) {
+    const theme = (0, material_1.useTheme)();
+    return (react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
+}
+exports.default = SVGBackground;
+//# sourceMappingURL=SVGBackground.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/DotplotView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAwC;AAExC,SAAwB,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,GAIP;IACC,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,OAAO,CACL,wCACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC;AAjBD,gCAiBC"}

package/dist/DotplotView/svgcomponents/SVGDotplotView.d.ts

@@ -0,0 +1,2 @@
+import { DotplotViewModel, ExportSvgOptions } from '../model';
+export declare function renderToSvg(model: DotplotViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/DotplotView/svgcomponents/SVGDotplotView.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 });
+exports.renderToSvg = void 0;
+const react_1 = __importDefault(require("react"));
+const server_1 = require("react-dom/server");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const Grid_1 = require("../components/Grid");
+const Axes_1 = require("../components/Axes");
+const SVGBackground_1 = __importDefault(require("./SVGBackground"));
+// render LGV to SVG
+async function renderToSvg(model, opts) {
+    var _a;
+    await (0, mobx_1.when)(() => model.initialized);
+    const { themeName = 'default', Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children) } = 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, borderX, viewWidth, viewHeight, tracks, height } = model;
+    const shift = 50;
+    const displayResults = await Promise.all(tracks.map(async (track) => {
+        const display = track.displays[0];
+        await (0, mobx_1.when)(() => (display.ready !== undefined ? display.ready : true));
+        return { track, result: await display.renderSvg({ ...opts, theme }) };
+    }));
+    const w = width + shift * 2;
+    // 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: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w, height].toString() },
+                react_1.default.createElement(SVGBackground_1.default, { width: w, height: height }),
+                react_1.default.createElement(Axes_1.VerticalAxisRaw, { model: model }),
+                react_1.default.createElement("g", { transform: `translate(${borderX} 0)` },
+                    react_1.default.createElement(Grid_1.GridRaw, { model: model }),
+                    react_1.default.createElement("defs", null,
+                        react_1.default.createElement("clipPath", { id: "clip-ruler" },
+                            react_1.default.createElement("rect", { x: 0, y: 0, width: viewWidth, height: viewHeight }))),
+                    react_1.default.createElement("g", { clipPath: "url(#clip-ruler)" }, displayResults.map(({ result }, i) => (react_1.default.createElement("g", { key: i }, result))))),
+                react_1.default.createElement("g", { transform: `translate(${borderX} ${viewHeight})` },
+                    react_1.default.createElement(Axes_1.HorizontalAxisRaw, { model: model }))))));
+}
+exports.renderToSvg = renderToSvg;
+//# sourceMappingURL=SVGDotplotView.js.map

package/dist/DotplotView/svgcomponents/SVGDotplotView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGDotplotView.js","sourceRoot":"","sources":["../../../src/DotplotView/svgcomponents/SVGDotplotView.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,6CAAuD;AACvD,+BAA2B;AAC3B,6CAA+C;AAC/C,4CAA6C;AAC7C,yCAAqD;AAIrD,6CAA4C;AAC5C,6CAAuE;AACvE,oEAA2C;AAE3C,oBAAoB;AACb,KAAK,UAAU,WAAW,CAC/B,KAAuB,EACvB,IAAsB;;IAEtB,MAAM,IAAA,WAAI,EAAC,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACnC,MAAM,EAAE,SAAS,GAAG,SAAS,EAAE,OAAO,GAAG,CAAC,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,8DAAG,QAAQ,CAAI,EAAE,GAC1E,IAAI,CAAA;IACN,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,MAAA,OAAO,CAAC,SAAS,wDAAK,SAAS,CAAC,CAAA;IAC9C,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,MAAM,cAAc,GAAG,MAAM,OAAO,CAAC,GAAG,CACtC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACvB,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACjC,MAAM,IAAA,WAAI,EAAC,GAAG,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;QACtE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,OAAO,CAAC,SAAS,CAAC,EAAE,GAAG,IAAI,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IACvE,CAAC,CAAC,CACH,CAAA;IACD,MAAM,CAAC,GAAG,KAAK,GAAG,KAAK,GAAG,CAAC,CAAA;IAE3B,wDAAwD;IACxD,OAAO,IAAA,6BAAoB,EACzB,8BAAC,wBAAa,IAAC,KAAK,EAAE,IAAA,uBAAkB,EAAC,KAAK,CAAC;QAC7C,8BAAC,OAAO;YACN,uCACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE;gBAErC,8BAAC,uBAAa,IAAC,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,GAAI;gBAC3C,8BAAC,sBAAe,IAAC,KAAK,EAAE,KAAK,GAAI;gBACjC,qCAAG,SAAS,EAAE,aAAa,OAAO,KAAK;oBACrC,8BAAC,cAAO,IAAC,KAAK,EAAE,KAAK,GAAI;oBACzB;wBACE,4CAAU,EAAE,EAAC,YAAY;4BACvB,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,EAAE,UAAU,GAAI,CACjD,CACN;oBACP,qCAAG,QAAQ,EAAC,kBAAkB,IAC3B,cAAc,CAAC,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CACrC,qCAAG,GAAG,EAAE,CAAC,IAAG,MAAM,CAAK,CACxB,CAAC,CACA,CACF;gBACJ,qCAAG,SAAS,EAAE,aAAa,OAAO,IAAI,UAAU,GAAG;oBACjD,8BAAC,wBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CACA,CACE,CACI,CACjB,CAAA;AACH,CAAC;AArDD,kCAqDC"}

package/dist/LaunchDotplotView.d.ts

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

package/dist/LaunchDotplotView.js

@@ -0,0 +1,45 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_1 = require("mobx");
+function LaunchDotplotView(pluginManager) {
+    pluginManager.addToExtensionPoint('LaunchView-DotplotView', 
+    // @ts-expect-error
+    async ({ session, views, tracks = [], }) => {
+        try {
+            const model = session.addView('DotplotView', {});
+            const assemblyNames = views.map(view => view.assembly);
+            (0, mobx_1.transaction)(() => {
+                model.setViews([
+                    { bpPerPx: 0.1, offsetPx: 0 },
+                    { bpPerPx: 0.1, offsetPx: 0 },
+                ]);
+                model.setAssemblyNames(assemblyNames[0], assemblyNames[1]);
+            });
+            // http://localhost:3000/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-{"views":[{"type":"DotplotView","views":[{"assembly":"volvox"},{"assembly":"volvox"}],"tracks":["volvox_fake_synteny"]}]}
+            const idsNotFound = [];
+            tracks.forEach(track => tryTrack(model, track, idsNotFound));
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
+        }
+        catch (e) {
+            session.notify(`${e}`, 'error');
+            throw e;
+        }
+    });
+}
+exports.default = LaunchDotplotView;
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}
+//# sourceMappingURL=LaunchDotplotView.js.map

package/dist/LaunchDotplotView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LaunchDotplotView.js","sourceRoot":"","sources":["../src/LaunchDotplotView.ts"],"names":[],"mappings":";;AAGA,+BAAkC;AAElC,SAAwB,iBAAiB,CAAC,aAA4B;IACpE,aAAa,CAAC,mBAAmB,CAC/B,wBAAwB;IACxB,mBAAmB;IACnB,KAAK,EAAE,EACL,OAAO,EACP,KAAK,EACL,MAAM,GAAG,EAAE,GAKZ,EAAE,EAAE;QACH,IAAI;YACF,MAAM,KAAK,GAAG,OAAO,CAAC,OAAO,CAAC,aAAa,EAAE,EAAE,CAAqB,CAAA;YACpE,MAAM,aAAa,GAAG,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAEtD,IAAA,kBAAW,EAAC,GAAG,EAAE;gBACf,KAAK,CAAC,QAAQ,CAAC;oBACb,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE;oBAC7B,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE;iBAC9B,CAAC,CAAA;gBACF,KAAK,CAAC,gBAAgB,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;YAC5D,CAAC,CAAC,CAAA;YAEF,wMAAwM;YAExM,MAAM,WAAW,GAAG,EAAc,CAAA;YAClC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC,CAAA;YAE5D,IAAI,WAAW,CAAC,MAAM,EAAE;gBACtB,MAAM,IAAI,KAAK,CACb,kCAAkC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAC1D,CAAA;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;YAC/B,MAAM,CAAC,CAAA;SACR;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAzCD,oCAyCC;AAED,SAAS,QAAQ,CACf,KAA2C,EAC3C,OAAe,EACf,WAAqB;IAErB,IAAI;QACF,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,CAAA;KACzB;IAAC,OAAO,CAAC,EAAE;QACV,IAAI,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,8BAA8B,CAAC,EAAE;YAChD,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;SAC1B;aAAM;YACL,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC"}

package/dist/ServerSideRenderedBlockContent.d.ts

@@ -0,0 +1,12 @@
+import React, { CSSProperties } from 'react';
+declare const _default: ({ model, style, }: {
+    model: {
+        error?: unknown;
+        message?: string;
+        filled?: boolean;
+        shouldDisplay?: boolean;
+        reactElement?: React.ReactElement;
+    };
+    style: CSSProperties;
+}) => React.JSX.Element | null;
+export default _default;

package/dist/ServerSideRenderedBlockContent.js

@@ -0,0 +1,87 @@
+"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 mui_1 = require("tss-react/mui");
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            paddingLeft: '0.6em',
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            textAlign: 'center',
+        },
+        blockMessage: {
+            backgroundColor: bg,
+            padding: '10px',
+        },
+        blockError: {
+            backgroundColor: bg,
+            padding: '10px',
+            color: 'red',
+        },
+    };
+});
+function LoadingMessage() {
+    // only show the loading message after 300ms to prevent excessive flickering
+    const [shown, setShown] = (0, react_1.useState)(false);
+    const { classes } = useStyles();
+    (0, react_1.useEffect)(() => {
+        const timeout = setTimeout(() => setShown(true), 300);
+        return () => clearTimeout(timeout);
+    }, []);
+    return shown ? (react_1.default.createElement("div", { className: classes.loading },
+        react_1.default.createElement(ui_1.LoadingEllipses, null))) : null;
+}
+function BlockMessage({ messageText }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement("div", { className: classes.blockMessage },
+        react_1.default.createElement(material_1.Typography, null, `${messageText}`)));
+}
+function BlockError({ error }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement("div", { className: classes.blockError },
+        react_1.default.createElement(material_1.Typography, null, `${error}`)));
+}
+exports.default = (0, mobx_react_1.observer)(function ({ model, style, }) {
+    if (model.error) {
+        return react_1.default.createElement(BlockError, { error: model.error, "data-testid": "reload_button" });
+    }
+    else if (model.message) {
+        return react_1.default.createElement(BlockMessage, { messageText: model.message });
+    }
+    else if (!model.filled) {
+        return react_1.default.createElement(LoadingMessage, null);
+    }
+    else if (model.shouldDisplay) {
+        return react_1.default.createElement("div", { style: style }, model.reactElement);
+    }
+    return null;
+});
+//# sourceMappingURL=ServerSideRenderedBlockContent.js.map

package/dist/ServerSideRenderedBlockContent.js.map

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

@@ -0,0 +1,23 @@
+import React from 'react';
+/**
+ * A block whose content is rendered outside of the main thread and hydrated by this
+ * component.
+ */
+declare function ServerSideSyntenyRendering({ model, }: {
+    model: {
+        imageData: string;
+        style: Record<string, string>;
+        renderProps: {
+            width: number;
+            height: number;
+            highResolutionScaling?: number;
+        };
+    };
+}): React.JSX.Element;
+declare namespace ServerSideSyntenyRendering {
+    var propTypes: {
+        model: import("prop-types").Validator<any>;
+    };
+}
+declare const _default: typeof ServerSideSyntenyRendering;
+export default _default;

package/dist/ServerSideSyntenyRendering.js

@@ -0,0 +1,54 @@
+"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 });
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const offscreenCanvasPonyfill_1 = require("@jbrowse/core/util/offscreenCanvasPonyfill");
+/**
+ * A block whose content is rendered outside of the main thread and hydrated by this
+ * component.
+ */
+function ServerSideSyntenyRendering({ model, }) {
+    const { imageData, style, renderProps } = model;
+    const { width, height, highResolutionScaling = 1 } = renderProps;
+    const featureCanvas = (0, react_1.useRef)(null);
+    const [done, setDone] = (0, react_1.useState)(false);
+    (0, react_1.useEffect)(() => {
+        if (!imageData) {
+            return;
+        }
+        const canvas = featureCanvas.current;
+        const context = canvas.getContext('2d');
+        (0, offscreenCanvasPonyfill_1.drawImageOntoCanvasContext)(imageData, context);
+        setDone(true);
+    }, [height, imageData, width]);
+    return (react_1.default.createElement("canvas", { "data-testid": `prerendered_canvas${done ? '_done' : ''}`, ref: featureCanvas, width: width * highResolutionScaling, height: height * highResolutionScaling, style: { width, height, ...style } }));
+}
+ServerSideSyntenyRendering.propTypes = {
+    model: mobx_react_1.PropTypes.observableObject.isRequired,
+};
+exports.default = (0, mobx_react_1.observer)(ServerSideSyntenyRendering);
+//# sourceMappingURL=ServerSideSyntenyRendering.js.map

package/dist/ServerSideSyntenyRendering.js.map

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

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

package/dist/index.js

@@ -0,0 +1,44 @@
+"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");
+// icons
+const Timeline_1 = __importDefault(require("@mui/icons-material/Timeline"));
+// locals
+const DotplotView_1 = __importDefault(require("./DotplotView"));
+const DotplotDisplay_1 = __importDefault(require("./DotplotDisplay"));
+const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
+const LaunchDotplotView_1 = __importDefault(require("./LaunchDotplotView"));
+const ComparativeRenderer_1 = __importDefault(require("./ComparativeRenderer"));
+const DotplotReadVsRef_1 = __importDefault(require("./DotplotReadVsRef"));
+class DotplotPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'DotplotPlugin';
+    }
+    install(pluginManager) {
+        (0, DotplotView_1.default)(pluginManager);
+        (0, DotplotDisplay_1.default)(pluginManager);
+        (0, DotplotRenderer_1.default)(pluginManager);
+        (0, LaunchDotplotView_1.default)(pluginManager);
+        (0, DotplotReadVsRef_1.default)(pluginManager);
+        // install our comparative rendering rpc callback
+        pluginManager.addRpcMethod(() => new ComparativeRenderer_1.default(pluginManager));
+    }
+    configure(pluginManager) {
+        if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {
+            pluginManager.rootModel.appendToSubMenu(['Add'], {
+                label: 'Dotplot view',
+                icon: Timeline_1.default,
+                onClick: (session) => {
+                    session.addView('DotplotView', {});
+                },
+            });
+        }
+    }
+}
+exports.default = DotplotPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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

@@ -0,0 +1,9 @@
+import { Feature } from '@jbrowse/core/util';
+export interface ReducedFeature {
+    refName: string;
+    start: number;
+    clipPos: number;
+    end: number;
+    seqLength: number;
+}
+export declare function getTag(f: Feature, tag: string): any;

package/dist/util.js

@@ -0,0 +1,9 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getTag = void 0;
+function getTag(f, tag) {
+    const tags = f.get('tags');
+    return tags ? tags[tag] : f.get(tag);
+}
+exports.getTag = getTag;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/ComparativeRenderer/index.d.ts

@@ -0,0 +1,27 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import ComparativeRenderer, { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+interface RenderArgs extends ComparativeRenderArgs {
+    adapterConfig: {};
+    rendererType: string;
+}
+interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
+    adapterConfig: {};
+    rendererType: string;
+}
+/**
+ * call a synteny renderer with the given args
+ * param views: a set of views that each contain a set of regions
+ * used instead of passing regions directly as in render()
+ */
+export default class ComparativeRender extends RpcMethodType {
+    name: string;
+    renameRegionsIfNeeded(args: RenderArgs, rend: ComparativeRenderer): Promise<ComparativeRenderArgs>;
+    getRenderer(rendererType: string): ComparativeRenderer;
+    serializeArguments(args: RenderArgs, rpcDriver: string): Promise<ComparativeRenderArgs | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized>;
+    execute(args: RenderArgsSerialized & {
+        signal?: RemoteAbortSignal;
+    }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
+    deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
+}
+export {};

package/esm/ComparativeRenderer/index.js

@@ -0,0 +1,53 @@
+import { checkAbortSignal } from '@jbrowse/core/util';
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+/**
+ * call a synteny renderer with the given args
+ * param views: a set of views that each contain a set of regions
+ * used instead of passing regions directly as in render()
+ */
+export default class ComparativeRender extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'ComparativeRender';
+    }
+    async renameRegionsIfNeeded(args, rend) {
+        return rend.renameRegionsIfNeeded(args);
+    }
+    getRenderer(rendererType) {
+        const pm = this.pluginManager;
+        return pm.getRendererType(rendererType);
+    }
+    async serializeArguments(args, rpcDriver) {
+        const { rendererType } = args;
+        const renderer = this.getRenderer(rendererType);
+        const n = (await super.serializeArguments(args, rpcDriver));
+        const result = await this.renameRegionsIfNeeded(n, renderer);
+        return rpcDriver === 'MainThreadRpcDriver'
+            ? result
+            : renderer.serializeArgsInClient(result);
+    }
+    async execute(args, rpcDriver) {
+        let deserializedArgs = args;
+        if (rpcDriver !== 'MainThreadRpcDriver') {
+            deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        }
+        const { sessionId, rendererType, signal } = deserializedArgs;
+        if (!sessionId) {
+            throw new Error('must pass a unique session id');
+        }
+        checkAbortSignal(signal);
+        const renderer = this.getRenderer(rendererType);
+        return rpcDriver === 'MainThreadRpcDriver'
+            ? renderer.render(deserializedArgs)
+            : renderer.renderInWorker(deserializedArgs);
+    }
+    async deserializeReturn(val, args, rpcDriver) {
+        const ret = (await super.deserializeReturn(val, args, rpcDriver));
+        if (rpcDriver === 'MainThreadRpcDriver') {
+            return ret;
+        }
+        const renderer = this.getRenderer(args.rendererType);
+        return renderer.deserializeResultsInClient(ret, args);
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/ComparativeRenderer/index.js.map

@@ -0,0 +1 @@
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package/esm/DotplotDisplay/components/DotplotDisplay.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { DotplotDisplayModel } from '../stateModelFactory';
+declare function DotplotDisplay(props: {
+    model: DotplotDisplayModel;
+    children?: React.ReactNode;
+}): React.JSX.Element;
+declare const _default: typeof DotplotDisplay;
+export default _default;

package/esm/DotplotDisplay/components/DotplotDisplay.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { getContainingView } from '@jbrowse/core/util';
+function DotplotDisplay(props) {
+    const { model, children } = props;
+    const { offsetX = 0, offsetY = 0 } = model.data || {};
+    const view = getContainingView(model);
+    const top = view.vview.offsetPx - offsetY;
+    const left = -(view.hview.offsetPx - offsetX);
+    return (React.createElement("div", { style: { position: 'relative' } },
+        React.createElement(model.ReactComponent2, { ...props, style: {
+                position: 'absolute',
+                top,
+                left,
+            } }),
+        children));
+}
+export default observer(DotplotDisplay);
+//# sourceMappingURL=DotplotDisplay.js.map

package/esm/DotplotDisplay/components/DotplotDisplay.js.map

@@ -0,0 +1 @@
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package/esm/DotplotDisplay/index.d.ts

@@ -0,0 +1,12 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pm: PluginManager) => void;
+export default _default;
+/**
+ * #config DotplotDisplay
+ */
+export declare function configSchemaFactory(pm: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    renderer: import("mobx-state-tree").IOptionalIType<any, [undefined]>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/esm/DotplotDisplay/index.js

@@ -0,0 +1,41 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+// locals
+import { stateModelFactory } from './stateModelFactory';
+import ReactComponent from './components/DotplotDisplay';
+export default (pm) => {
+    pm.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pm);
+        return new DisplayType({
+            name: 'DotplotDisplay',
+            displayName: 'Dotplot display',
+            configSchema,
+            stateModel: stateModelFactory(configSchema),
+            trackType: 'SyntenyTrack',
+            viewType: 'DotplotView',
+            ReactComponent,
+        });
+    });
+};
+/**
+ * #config DotplotDisplay
+ */
+export function configSchemaFactory(pm) {
+    return ConfigurationSchema('DotplotDisplay', {
+        /**
+         * #slot
+         */
+        renderer: types.optional(pm.pluggableConfigSchemaType('renderer'), {
+            type: 'DotplotRenderer',
+        }),
+    }, {
+        /**
+         * #identifier
+         */
+        explicitIdentifier: 'displayId',
+        explicitlyTyped: true,
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/DotplotDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/DotplotDisplay/index.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAGzE,SAAS;AACT,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAA;AACvD,OAAO,cAAc,MAAM,6BAA6B,CAAA;AAExD,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,cAAc,CAAC,GAAG,EAAE;QACrB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,iBAAiB;YAC9B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,aAAa;YACvB,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,EAAO;IACzC,OAAO,mBAAmB,CACxB,gBAAgB,EAChB;QACE;;WAEG;QACH,QAAQ,EAAE,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC,yBAAyB,CAAC,UAAU,CAAC,EAAE;YACjE,IAAI,EAAE,iBAAiB;SACxB,CAAC;KACH,EACD;QACE;;WAEG;QACH,kBAAkB,EAAE,WAAW;QAC/B,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

package/esm/DotplotDisplay/renderDotplotBlock.d.ts

@@ -0,0 +1,11 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function renderBlockData(self: IAnyStateTreeNode): {
+    rendererType: any;
+    rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    renderProps: any;
+} | undefined;
+export declare function renderBlockEffect(props?: ReturnType<typeof renderBlockData>): Promise<{
+    reactElement: any;
+    data: any;
+    renderingComponent: any;
+} | undefined>;