@jbrowse/plugin-dotplot-view 3.6.5 → 4.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-dotplot-view",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 dotplot view",
   "keywords": [
     "jbrowse",
@@ -15,49 +15,42 @@
     "directory": "plugins/dotplot-view"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/dotplot-view",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-alignments": "^3.6.5",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "@mui/x-data-grid": "^8.0.0",
-    "@types/file-saver": "^2.0.1",
-    "file-saver": "^2.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-data-grid": "^8.23.0",
+    "@types/file-saver-es": "^2.0.3",
+    "file-saver-es": "^2.0.5",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-alignments": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/dotplot-view",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/ComparativeRenderer/index.d.ts

@@ -1,22 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-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;
-}
-interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
-    adapterConfig: Record<string, unknown>;
-    rendererType: string;
-}
-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 & {
-        stopToken?: string;
-    }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
-    deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
-}
-export {};

package/dist/ComparativeRenderer/index.js

@@ -1,53 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-class ComparativeRender extends RpcMethodType_1.default {
-    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, stopToken } = deserializedArgs;
-        if (!sessionId) {
-            throw new Error('must pass a unique session id');
-        }
-        (0, stopToken_1.checkStopToken)(stopToken);
-        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);
-    }
-}
-exports.default = ComparativeRender;

package/dist/DotplotDisplay/components/DotplotDisplay.d.ts

@@ -1,6 +0,0 @@
-import type { DotplotDisplayModel } from '../stateModelFactory';
-declare const DotplotDisplay: (props: {
-    model: DotplotDisplayModel;
-    children?: React.ReactNode;
-}) => import("react/jsx-runtime").JSX.Element;
-export default DotplotDisplay;

package/dist/DotplotDisplay/components/DotplotDisplay.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-const DotplotDisplay = (0, mobx_react_1.observer)(function DotplotDisplay(props) {
-    const { model, children } = props;
-    const { offsetX = 0, offsetY = 0 } = model.data || {};
-    const view = (0, util_1.getContainingView)(model);
-    const top = view.vview.offsetPx - offsetY;
-    const left = -(view.hview.offsetPx - offsetX);
-    return ((0, jsx_runtime_1.jsxs)("div", { style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)(model.ReactComponent2, { ...props, style: {
-                    position: 'absolute',
-                    top,
-                    left,
-                } }), children] }));
-});
-exports.default = DotplotDisplay;

package/dist/DotplotDisplay/index.d.ts

@@ -1,5 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function DotplotDisplayF(pm: PluginManager): void;
-export declare function configSchemaFactory(pm: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("mobx-state-tree").IOptionalIType<any, [undefined]>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/dist/DotplotDisplay/index.js

@@ -1,36 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = DotplotDisplayF;
-exports.configSchemaFactory = configSchemaFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const DotplotDisplay_1 = __importDefault(require("./components/DotplotDisplay"));
-const stateModelFactory_1 = require("./stateModelFactory");
-function DotplotDisplayF(pm) {
-    pm.addDisplayType(() => {
-        const configSchema = configSchemaFactory(pm);
-        return new DisplayType_1.default({
-            name: 'DotplotDisplay',
-            displayName: 'Dotplot display',
-            configSchema,
-            stateModel: (0, stateModelFactory_1.stateModelFactory)(configSchema),
-            trackType: 'SyntenyTrack',
-            viewType: 'DotplotView',
-            ReactComponent: DotplotDisplay_1.default,
-        });
-    });
-}
-function configSchemaFactory(pm) {
-    return (0, configuration_1.ConfigurationSchema)('DotplotDisplay', {
-        renderer: mobx_state_tree_1.types.optional(pm.pluggableConfigSchemaType('renderer'), {
-            type: 'DotplotRenderer',
-        }),
-    }, {
-        explicitIdentifier: 'displayId',
-        explicitlyTyped: true,
-    });
-}

package/dist/DotplotDisplay/renderDotplotBlock.d.ts

@@ -1,11 +0,0 @@
-import type { 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>;

package/dist/DotplotDisplay/renderDotplotBlock.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderBlockData = renderBlockData;
-exports.renderBlockEffect = renderBlockEffect;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function renderBlockData(self) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const { rendererType } = self;
-    const { adapterConfig } = self;
-    const parent = (0, util_1.getContainingView)(self);
-    (0, configuration_1.readConfObject)(self.configuration);
-    (0, mobx_state_tree_1.getSnapshot)(parent);
-    if (parent.initialized) {
-        const { viewWidth, viewHeight, borderSize, borderX, borderY } = parent;
-        return {
-            rendererType,
-            rpcManager,
-            renderProps: {
-                ...self.renderProps(),
-                view: structuredClone((0, mobx_state_tree_1.getSnapshot)(parent)),
-                width: viewWidth,
-                height: viewHeight,
-                borderSize,
-                borderX,
-                borderY,
-                adapterConfig,
-                rendererType: rendererType.name,
-                sessionId: (0, tracks_1.getRpcSessionId)(self),
-                timeout: 1000000,
-            },
-        };
-    }
-    return undefined;
-}
-async function renderBlockEffect(props) {
-    if (!props) {
-        return;
-    }
-    const { rendererType, rpcManager, renderProps } = props;
-    const { reactElement, ...data } = await rendererType.renderInClient(rpcManager, renderProps);
-    return {
-        reactElement,
-        data,
-        renderingComponent: rendererType.ReactComponent,
-    };
-}

package/dist/DotplotDisplay/stateModelFactory.d.ts

@@ -1,102 +0,0 @@
-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>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"DotplotDisplay">;
-    configuration: AnyConfigurationSchemaType;
-}, {
-    rendererTypeName: string;
-    error: unknown;
-    message: string | undefined;
-} & {
-    readonly RenderingComponent: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: () => void;
-        blockState?: Record<string, any>;
-    }>;
-    readonly DisplayBlurb: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
-    readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
-} & {
-    stopToken: string | undefined;
-    warnings: {
-        message: string;
-        effect: string;
-    }[];
-    filled: boolean;
-    data: any;
-    reactElement: React.ReactElement | undefined;
-    message: string | undefined;
-    renderingComponent: any;
-    ReactComponent2: React.FC<any>;
-} & {
-    readonly shouldDisplay: boolean;
-    readonly rendererTypeName: any;
-    renderProps(): any;
-} & {
-    renderSvg(opts: ExportSvgOptions & {
-        theme?: ThemeOptions;
-    }): Promise<import("react/jsx-runtime").JSX.Element | null>;
-} & {
-    afterAttach(): void;
-    setLoading(stopToken?: string): void;
-    setMessage(messageText: string): void;
-    setRendered(args?: {
-        data: any;
-        reactElement: React.ReactElement;
-        renderingComponent: React.Component;
-    }): void;
-    setError(error: unknown): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type DotplotDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type DotplotDisplayModel = Instance<DotplotDisplayStateModel>;

package/dist/DotplotDisplay/stateModelFactory.js

@@ -1,119 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = stateModelFactory;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const ServerSideRenderedBlockContent_1 = __importDefault(require("../ServerSideRenderedBlockContent"));
-const renderDotplotBlock_1 = require("./renderDotplotBlock");
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('DotplotDisplay', models_1.BaseDisplay, mobx_state_tree_1.types
-        .model({
-        type: mobx_state_tree_1.types.literal('DotplotDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-    })
-        .volatile(() => ({
-        stopToken: undefined,
-        warnings: [],
-        filled: false,
-        data: undefined,
-        reactElement: undefined,
-        message: undefined,
-        renderingComponent: undefined,
-        ReactComponent2: ServerSideRenderedBlockContent_1.default,
-    })))
-        .views(self => ({
-        get shouldDisplay() {
-            const { vview, hview } = (0, util_1.getContainingView)(self);
-            return (vview.bpPerPx === self.data.bpPerPxY &&
-                hview.bpPerPx === self.data.bpPerPxX);
-        },
-        get rendererTypeName() {
-            return (0, configuration_1.getConf)(self, ['renderer', 'type']);
-        },
-        renderProps() {
-            return {
-                ...(0, tracks_1.getParentRenderProps)(self),
-                rpcDriverName: self.rpcDriverName,
-                displayModel: self,
-                config: self.configuration.renderer,
-            };
-        },
-    }))
-        .views(self => ({
-        async renderSvg(opts) {
-            const props = (0, renderDotplotBlock_1.renderBlockData)(self);
-            if (!props) {
-                return null;
-            }
-            const { rendererType, rpcManager, renderProps } = props;
-            const rendering = await rendererType.renderInClient(rpcManager, {
-                ...renderProps,
-                exportSVG: opts,
-                theme: opts.theme || renderProps.theme,
-            });
-            const { hview, vview } = (0, util_1.getContainingView)(self);
-            const offX = -hview.offsetPx + rendering.offsetX;
-            const offY = -vview.offsetPx + rendering.offsetY;
-            return ((0, jsx_runtime_1.jsx)("g", { transform: `translate(${offX} ${-offY})`, children: (0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: rendering }) }));
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, util_1.makeAbortableReaction)(self, () => (0, renderDotplotBlock_1.renderBlockData)(self), blockData => (0, renderDotplotBlock_1.renderBlockEffect)(blockData), {
-                name: `${self.type} ${self.id} rendering`,
-                delay: 500,
-                fireImmediately: true,
-            }, this.setLoading, this.setRendered, this.setError);
-        },
-        setLoading(stopToken) {
-            self.filled = false;
-            self.message = undefined;
-            self.reactElement = undefined;
-            self.data = undefined;
-            self.error = undefined;
-            self.renderingComponent = undefined;
-            self.stopToken = stopToken;
-        },
-        setMessage(messageText) {
-            self.filled = false;
-            self.message = messageText;
-            self.reactElement = undefined;
-            self.data = undefined;
-            self.error = undefined;
-            self.renderingComponent = undefined;
-            self.stopToken = undefined;
-        },
-        setRendered(args) {
-            if (args === undefined) {
-                return;
-            }
-            const { data, reactElement, renderingComponent } = args;
-            self.warnings = data.warnings;
-            self.filled = true;
-            self.message = undefined;
-            self.reactElement = reactElement;
-            self.data = data;
-            self.error = undefined;
-            self.renderingComponent = renderingComponent;
-            self.stopToken = undefined;
-        },
-        setError(error) {
-            console.error(error);
-            self.filled = false;
-            self.message = undefined;
-            self.reactElement = undefined;
-            self.data = undefined;
-            self.error = error;
-            self.renderingComponent = undefined;
-            self.stopToken = undefined;
-        },
-    }));
-}

package/dist/DotplotReadVsRef/DotplotReadVsRef.d.ts

@@ -1,3 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-import type { LinearPileupDisplayModel } from '@jbrowse/plugin-alignments';
-export declare function onClick(feature: Feature, self: LinearPileupDisplayModel): void;

package/dist/DotplotReadVsRef/DotplotReadVsRef.js

@@ -1,100 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.onClick = onClick;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const { featurizeSA, getClip, getLength, getLengthSansClipping } = plugin_alignments_1.MismatchParser;
-function onClick(feature, self) {
-    var _a;
-    const session = (0, util_1.getSession)(self);
-    try {
-        const cigar = feature.get('CIGAR');
-        const clipPos = getClip(cigar, 1);
-        const flags = feature.get('flags');
-        const strand = feature.get('strand');
-        const readName = feature.get('name');
-        const readAssembly = `${readName}_assembly_${Date.now()}`;
-        const { parentTrack } = self;
-        const [trackAssembly] = (0, configuration_1.getConf)(parentTrack, 'assemblyNames');
-        const assemblyNames = [trackAssembly, readAssembly];
-        const trackId = `track-${Date.now()}`;
-        const trackName = `${readName}_vs_${trackAssembly}`;
-        const SA = (_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA;
-        const SA2 = featurizeSA(SA, feature.id(), strand, readName, true);
-        const totalLength = getLength(flags & 2048 ? SA2[0].CIGAR : cigar);
-        const features = [
-            {
-                ...feature.toJSON(),
-                strand: 1,
-                mate: {
-                    refName: readName,
-                    start: clipPos,
-                    end: clipPos + getLengthSansClipping(cigar),
-                },
-            },
-            ...SA2,
-        ].sort((a, b) => a.clipPos - b.clipPos);
-        session.addView('DotplotView', {
-            type: 'DotplotView',
-            hview: {
-                offsetPx: 0,
-                bpPerPx: (0, util_1.sum)(features.map(a => a.end - a.start)) / 800,
-                displayedRegions: (0, util_1.gatherOverlaps)(features.map((f, index) => {
-                    const { start, end, refName } = f;
-                    return {
-                        start,
-                        end,
-                        refName,
-                        index,
-                        assemblyName: trackAssembly,
-                    };
-                })),
-            },
-            vview: {
-                offsetPx: 0,
-                bpPerPx: totalLength / 400,
-                minimumBlockWidth: 0,
-                interRegionPaddingWidth: 0,
-                displayedRegions: [
-                    {
-                        assemblyName: readAssembly,
-                        start: 0,
-                        end: totalLength,
-                        refName: readName,
-                    },
-                ],
-            },
-            viewTrackConfigs: [
-                {
-                    type: 'SyntenyTrack',
-                    assemblyNames,
-                    adapter: {
-                        type: 'FromConfigAdapter',
-                        features,
-                    },
-                    trackId,
-                    name: trackName,
-                },
-            ],
-            assemblyNames,
-            tracks: [
-                {
-                    configuration: trackId,
-                    type: 'SyntenyTrack',
-                    displays: [
-                        {
-                            type: 'DotplotDisplay',
-                            configuration: `${trackId}-DotplotDisplay`,
-                        },
-                    ],
-                },
-            ],
-            displayName: `${readName} vs ${trackAssembly}`,
-        });
-    }
-    catch (e) {
-        console.error(e);
-        session.notifyError(`${e}`, e);
-    }
-}

package/dist/DotplotReadVsRef/index.d.ts

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

package/dist/DotplotReadVsRef/index.js

@@ -1,41 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = DotplotReadVsRefMenuItem;
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-const DotplotReadVsRef_1 = require("./DotplotReadVsRef");
-function DotplotReadVsRefMenuItem(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
-        if (pluggableElement.name === 'LinearPileupDisplay') {
-            const { stateModel } = pluggableElement;
-            const newStateModel = stateModel.extend((self) => {
-                const superContextMenuItems = self.contextMenuItems;
-                return {
-                    views: {
-                        contextMenuItems() {
-                            const feature = self.contextMenuFeature;
-                            return [
-                                ...superContextMenuItems(),
-                                ...(feature
-                                    ? [
-                                        {
-                                            label: 'Dotplot of read vs ref',
-                                            icon: Add_1.default,
-                                            onClick: () => {
-                                                (0, DotplotReadVsRef_1.onClick)(feature, self);
-                                            },
-                                        },
-                                    ]
-                                    : []),
-                            ];
-                        },
-                    },
-                };
-            });
-            pluggableElement.stateModel = newStateModel;
-        }
-        return pluggableElement;
-    });
-}