@jbrowse/plugin-dotplot-view 2.17.0 → 3.0.0

package/dist/LaunchDotplotView.js

@@ -3,9 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchDotplotView;
 const mobx_1 = require("mobx");
 function LaunchDotplotView(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-DotplotView', 
-    // @ts-expect-error
-    async ({ session, views, tracks = [], }) => {
+    pluginManager.addToExtensionPoint('LaunchView-DotplotView', async ({ session, views, tracks = [], }) => {
         try {
             const model = session.addView('DotplotView', {});
             const assemblyNames = views.map(view => view.assembly);
@@ -16,7 +14,6 @@ function LaunchDotplotView(pluginManager) {
                 ]);
                 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);

package/dist/ServerSideRenderedBlockContent.d.ts

@@ -1,4 +1,4 @@
-import React, { CSSProperties } from 'react';
+import type { CSSProperties } from 'react';
 declare const ServerSideRenderedDotplotContent: ({ model, style, }: {
     model: {
         error?: unknown;
@@ -8,5 +8,5 @@ declare const ServerSideRenderedDotplotContent: ({ model, style, }: {
         reactElement?: React.ReactElement;
     };
     style: CSSProperties;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default ServerSideRenderedDotplotContent;

package/dist/ServerSideRenderedBlockContent.js

@@ -1,33 +1,11 @@
 "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 jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => {
     const bg = theme.palette.action.disabledBackground;
     return {
@@ -49,7 +27,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
     };
 });
 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)(() => {
@@ -60,31 +37,28 @@ function LoadingMessage() {
             clearTimeout(timeout);
         };
     }, []);
-    return shown ? (react_1.default.createElement("div", { className: classes.loading },
-        react_1.default.createElement(ui_1.LoadingEllipses, null))) : null;
+    return shown ? ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}) })) : 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)));
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.blockMessage, children: (0, jsx_runtime_1.jsx)(material_1.Typography, { children: messageText }) }));
 }
 function BlockError({ error }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement("div", { className: classes.blockError },
-        react_1.default.createElement(material_1.Typography, null, `${error}`)));
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.blockError, children: (0, jsx_runtime_1.jsx)(material_1.Typography, { children: `${error}` }) }));
 }
 const ServerSideRenderedDotplotContent = (0, mobx_react_1.observer)(function ({ model, style, }) {
     if (model.error) {
-        return react_1.default.createElement(BlockError, { error: model.error, "data-testid": "reload_button" });
+        return (0, jsx_runtime_1.jsx)(BlockError, { error: model.error, "data-testid": "reload_button" });
     }
     else if (model.message) {
-        return react_1.default.createElement(BlockMessage, { messageText: model.message });
+        return (0, jsx_runtime_1.jsx)(BlockMessage, { messageText: model.message });
     }
     else if (!model.filled) {
-        return react_1.default.createElement(LoadingMessage, null);
+        return (0, jsx_runtime_1.jsx)(LoadingMessage, {});
     }
     else if (model.shouldDisplay) {
-        return react_1.default.createElement("div", { style: style }, model.reactElement);
+        return (0, jsx_runtime_1.jsx)("div", { style: style, children: model.reactElement });
     }
     return null;
 });

package/dist/ServerSideSyntenyRendering.d.ts

@@ -1,8 +1,3 @@
-import React from 'react';
-/**
- * A block whose content is rendered outside of the main thread and hydrated by
- * this component.
- */
 interface ModelType {
     imageData: string;
     style: Record<string, string>;
@@ -14,5 +9,5 @@ interface ModelType {
 }
 declare const ServerSideSyntenyRendering: ({ model, }: {
     model: ModelType;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ServerSideSyntenyRendering;

package/dist/ServerSideSyntenyRendering.js

@@ -1,31 +1,9 @@
 "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 mobx_react_1 = require("mobx-react");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const offscreenCanvasPonyfill_1 = require("@jbrowse/core/util/offscreenCanvasPonyfill");
+const mobx_react_1 = require("mobx-react");
 const ServerSideSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, }) {
     const { imageData, style, renderProps } = model;
     const { width, height, highResolutionScaling = 1 } = renderProps;
@@ -40,6 +18,6 @@ const ServerSideSyntenyRendering = (0, mobx_react_1.observer)(function ({ model,
         (0, offscreenCanvasPonyfill_1.drawImageOntoCanvasContext)(imageData, context);
         setDone(true);
     }, [imageData]);
-    return (react_1.default.createElement("canvas", { "data-testid": `prerendered_canvas${done ? '_done' : ''}`, ref: featureCanvas, width: width * highResolutionScaling, height: height * highResolutionScaling, style: { width, height, ...style } }));
+    return ((0, jsx_runtime_1.jsx)("canvas", { "data-testid": `prerendered_canvas${done ? '_done' : ''}`, ref: featureCanvas, width: width * highResolutionScaling, height: height * highResolutionScaling, style: { width, height, ...style } }));
 });
 exports.default = ServerSideSyntenyRendering;

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class DotplotPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -5,15 +5,13 @@ var __importDefault = (this && this.__importDefault) || function (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 ComparativeRenderer_1 = __importDefault(require("./ComparativeRenderer"));
 const DotplotDisplay_1 = __importDefault(require("./DotplotDisplay"));
+const DotplotReadVsRef_1 = __importDefault(require("./DotplotReadVsRef"));
 const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
+const DotplotView_1 = __importDefault(require("./DotplotView"));
 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);
@@ -25,7 +23,6 @@ class DotplotPlugin extends Plugin_1.default {
         (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) {

package/dist/util.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export interface ReducedFeature {
     refName: string;
     start: number;

package/esm/ComparativeRenderer/index.d.ts

@@ -1,6 +1,6 @@
 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';
+import type { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
+import type ComparativeRenderer from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
 interface RenderArgs extends ComparativeRenderArgs {
     adapterConfig: Record<string, unknown>;
     rendererType: string;
@@ -9,18 +9,13 @@ interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
     adapterConfig: Record<string, unknown>;
     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;
+        stopToken?: string;
     }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
     deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
 }

package/esm/ComparativeRenderer/index.js

@@ -1,10 +1,5 @@
-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()
- */
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 export default class ComparativeRender extends RpcMethodType {
     constructor() {
         super(...arguments);
@@ -31,11 +26,11 @@ export default class ComparativeRender extends RpcMethodType {
         if (rpcDriver !== 'MainThreadRpcDriver') {
             deserializedArgs = await this.deserializeArguments(args, rpcDriver);
         }
-        const { sessionId, rendererType, signal } = deserializedArgs;
+        const { sessionId, rendererType, stopToken } = deserializedArgs;
         if (!sessionId) {
             throw new Error('must pass a unique session id');
         }
-        checkAbortSignal(signal);
+        checkStopToken(stopToken);
         const renderer = this.getRenderer(rendererType);
         return rpcDriver === 'MainThreadRpcDriver'
             ? renderer.render(deserializedArgs)

package/esm/DotplotDisplay/components/DotplotDisplay.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { DotplotDisplayModel } from '../stateModelFactory';
+import type { DotplotDisplayModel } from '../stateModelFactory';
 declare const DotplotDisplay: (props: {
     model: DotplotDisplayModel;
     children?: React.ReactNode;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DotplotDisplay;

package/esm/DotplotDisplay/components/DotplotDisplay.js

@@ -1,18 +1,16 @@
-import React from 'react';
-import { observer } from 'mobx-react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
 const DotplotDisplay = observer(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));
+    return (_jsxs("div", { style: { position: 'relative' }, children: [_jsx(model.ReactComponent2, { ...props, style: {
+                    position: 'absolute',
+                    top,
+                    left,
+                } }), children] }));
 });
 export default DotplotDisplay;

package/esm/DotplotDisplay/index.d.ts

@@ -1,11 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function DotplotDisplayF(pm: PluginManager): void;
-/**
- * #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

@@ -1,9 +1,8 @@
 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 { types } from 'mobx-state-tree';
 import ReactComponent from './components/DotplotDisplay';
+import { stateModelFactory } from './stateModelFactory';
 export default function DotplotDisplayF(pm) {
     pm.addDisplayType(() => {
         const configSchema = configSchemaFactory(pm);
@@ -18,21 +17,12 @@ export default function DotplotDisplayF(pm) {
         });
     });
 }
-/**
- * #config DotplotDisplay
- */
 export function configSchemaFactory(pm) {
     return ConfigurationSchema('DotplotDisplay', {
-        /**
-         * #slot
-         */
         renderer: types.optional(pm.pluggableConfigSchemaType('renderer'), {
             type: 'DotplotRenderer',
         }),
     }, {
-        /**
-         * #identifier
-         */
         explicitIdentifier: 'displayId',
         explicitlyTyped: true,
     });

package/esm/DotplotDisplay/renderDotplotBlock.d.ts

@@ -1,4 +1,4 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function renderBlockData(self: IAnyStateTreeNode): {
     rendererType: any;
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;

package/esm/DotplotDisplay/renderDotplotBlock.js

@@ -1,15 +1,12 @@
-import clone from 'clone';
 import { readConfObject } from '@jbrowse/core/configuration';
+import { getContainingView, getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { getSnapshot } from 'mobx-state-tree';
-import { getContainingView, getSession } from '@jbrowse/core/util';
 export function renderBlockData(self) {
     const { rpcManager } = getSession(self);
     const { rendererType } = self;
     const { adapterConfig } = self;
     const parent = getContainingView(self);
-    // Alternative to readConfObject(config) is below used because renderProps is
-    // something under our control.  Compare to serverSideRenderedBlock
     readConfObject(self.configuration);
     getSnapshot(parent);
     if (parent.initialized) {
@@ -19,7 +16,7 @@ export function renderBlockData(self) {
             rpcManager,
             renderProps: {
                 ...self.renderProps(),
-                view: clone(getSnapshot(parent)),
+                view: structuredClone(getSnapshot(parent)),
                 width: viewWidth,
                 height: viewHeight,
                 borderSize,
@@ -28,7 +25,7 @@ export function renderBlockData(self) {
                 adapterConfig,
                 rendererType: rendererType.name,
                 sessionId: getRpcSessionId(self),
-                timeout: 1000000, // 10000,
+                timeout: 1000000,
             },
         };
     }

package/esm/DotplotDisplay/stateModelFactory.d.ts

@@ -1,36 +1,20 @@
-import React from 'react';
-import { ThemeOptions } from '@mui/material';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ExportSvgOptions } from '../DotplotView/model';
-/**
- * #stateModel DotplotDisplay
- * #category display
- */
+import type { ExportSvgOptions } from '../DotplotView/model';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { ThemeOptions } from '@mui/material';
+import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"DotplotDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown;
     message: string | undefined;
 } & {
-    readonly RenderingComponent: React.
-    /**
-     * #stateModel DotplotDisplay
-     * #category display
-     */
-    FC<{
+    readonly RenderingComponent: React.FC<{
         model: {
             id: string;
             type: string;
@@ -84,11 +68,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    stopToken: string | undefined;
     warnings: {
         message: string;
         effect: string;
     }[];
-    renderInProgress: AbortController | undefined;
     filled: boolean;
     data: any;
     reactElement: React.ReactElement | undefined;
@@ -97,42 +81,21 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     ReactComponent2: React.FC<any>;
 } & {
     readonly shouldDisplay: boolean;
-    /**
-     * #getter
-     */
     readonly rendererTypeName: any;
-    /**
-     * #method
-     */
     renderProps(): any;
 } & {
-    /**
-     * #method
-     */
     renderSvg(opts: ExportSvgOptions & {
         theme?: ThemeOptions;
-    }): Promise<React.JSX.Element | null>;
+    }): Promise<import("react/jsx-runtime").JSX.Element | null>;
 } & {
     afterAttach(): void;
-    /**
-     * #action
-     */
-    setLoading(abortController: AbortController): void;
-    /**
-     * #action
-     */
+    setLoading(stopToken?: string): void;
     setMessage(messageText: string): void;
-    /**
-     * #action
-     */
     setRendered(args?: {
         data: any;
         reactElement: React.ReactElement;
         renderingComponent: React.Component;
     }): void;
-    /**
-     * #action
-     */
     setError(error: unknown): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type DotplotDisplayStateModel = ReturnType<typeof stateModelFactory>;