@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/LinearReadArcsDisplay/index.d.ts

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

package/dist/LinearReadArcsDisplay/index.js

@@ -1,58 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __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 });
-exports.default = register;
-const react_1 = require("react");
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function register(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearReadArcsDisplay',
-            displayName: 'Read arc display',
-            configSchema,
-            stateModel: (0, model_1.default)(configSchema),
-            trackType: 'AlignmentsTrack',
-            viewType: 'LinearGenomeView',
-            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ReactComponent')))),
-        });
-    });
-}

package/dist/LinearReadArcsDisplay/model.d.ts

@@ -1,189 +0,0 @@
-import type React from 'react';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Instance } from 'mobx-state-tree';
-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>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    jitter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    drawInter: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawLongRange: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, {
-    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;
-} & {
-    scrollTop: number;
-} & {
-    readonly height: number;
-} & {
-    setScrollTop(scrollTop: number): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-} & {
-    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
-    currStatsBpPerPx: number;
-} & {
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly featureDensityStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    afterAttach(): void;
-} & {
-    setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    clearFeatureDensityStats(): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
-} & {
-    readonly statsReadyAndRegionNotTooLarge: boolean;
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
-} & {
-    loading: boolean;
-    chainData: import("../shared/fetchChains").ChainData | undefined;
-    lastDrawnOffsetPx: number | undefined;
-    lastDrawnBpPerPx: number;
-    ref: HTMLCanvasElement | null;
-} & {
-    setLastDrawnOffsetPx(n: number): void;
-    setLastDrawnBpPerPx(n: number): void;
-    setLoading(f: boolean): void;
-    setRef(ref: HTMLCanvasElement | null): void;
-    setColorScheme(colorBy: {
-        type: string;
-    }): void;
-    setChainData(args: import("../shared/fetchChains").ChainData): void;
-    setFilterBy(filter: import("../shared/types").FilterBy): void;
-} & {
-    readonly drawn: boolean;
-} & {
-    readonly colorBy: any;
-    readonly filterBy: any;
-} & {
-    reload(): void;
-    setDrawInter(f: boolean): void;
-    setDrawLongRange(f: boolean): void;
-    setLineWidth(n: number): void;
-    setJitter(n: number): void;
-} & {
-    readonly lineWidthSetting: any;
-    readonly jitterVal: number;
-} & {
-    renderProps(): any;
-    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    } | {
-        label: string;
-        subMenu: {
-            type: string;
-            checked: boolean;
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: boolean;
-        onClick: () => void;
-        subMenu?: undefined;
-    })[];
-} & {
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<React.ReactNode>;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type LinearReadArcsDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type LinearReadArcsDisplayModel = Instance<LinearReadArcsDisplayStateModel>;
-export default stateModelFactory;

package/dist/LinearReadArcsDisplay/model.js

@@ -1,199 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const LinearReadDisplayBaseMixin_1 = require("../shared/LinearReadDisplayBaseMixin");
-const menuItems_1 = require("../shared/menuItems");
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearReadArcsDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), (0, LinearReadDisplayBaseMixin_1.LinearReadDisplayBaseMixin)(), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearReadArcsDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        lineWidth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        jitter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        drawInter: true,
-        drawLongRange: true,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-    }))
-        .actions(self => ({
-        reload() {
-            self.error = undefined;
-        },
-        setDrawInter(f) {
-            self.drawInter = f;
-        },
-        setDrawLongRange(f) {
-            self.drawLongRange = f;
-        },
-        setLineWidth(n) {
-            self.lineWidth = n;
-        },
-        setJitter(n) {
-            self.jitter = n;
-        },
-    }))
-        .views(self => ({
-        get lineWidthSetting() {
-            var _a;
-            return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'lineWidth');
-        },
-        get jitterVal() {
-            var _a;
-            return (_a = self.jitter) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jitter');
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            renderProps() {
-                return {
-                    ...superRenderProps(),
-                    notReady: !self.chainData,
-                };
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    (0, menuItems_1.getFilterByMenuItem)(self),
-                    {
-                        label: 'Line width',
-                        subMenu: [
-                            {
-                                label: 'Thin',
-                                onClick: () => {
-                                    self.setLineWidth(1);
-                                },
-                            },
-                            {
-                                label: 'Bold',
-                                onClick: () => {
-                                    self.setLineWidth(2);
-                                },
-                            },
-                            {
-                                label: 'Extra bold',
-                                onClick: () => {
-                                    self.setLineWidth(5);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Jitter x-positions',
-                        subMenu: [
-                            {
-                                type: 'checkbox',
-                                checked: self.jitterVal === 0,
-                                label: 'None',
-                                onClick: () => {
-                                    self.setJitter(0);
-                                },
-                            },
-                            {
-                                type: 'checkbox',
-                                checked: self.jitterVal === 2,
-                                label: 'Small',
-                                onClick: () => {
-                                    self.setJitter(2);
-                                },
-                            },
-                            {
-                                type: 'checkbox',
-                                checked: self.jitterVal === 10,
-                                label: 'Large',
-                                onClick: () => {
-                                    self.setJitter(10);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Draw inter-region vertical lines',
-                        type: 'checkbox',
-                        checked: self.drawInter,
-                        onClick: () => {
-                            self.setDrawInter(!self.drawInter);
-                        },
-                    },
-                    {
-                        label: 'Draw long range connections',
-                        type: 'checkbox',
-                        checked: self.drawLongRange,
-                        onClick: () => {
-                            self.setDrawLongRange(!self.drawLongRange);
-                        },
-                    },
-                    (0, menuItems_1.getColorSchemeMenuItem)(self),
-                ];
-            },
-        };
-    })
-        .views(self => ({
-        async renderSvg(opts) {
-            const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
-            const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
-            return renderSvg(self, opts, drawFeats);
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('../shared/afterAttach')));
-                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
-                    doAfterAttach(self, drawFeats);
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            })();
-        },
-    }));
-}
-exports.default = stateModelFactory;

package/dist/LinearReadArcsDisplay/util.d.ts

@@ -1,2 +0,0 @@
-import type { ChainData } from '../shared/fetchChains';
-export declare function hasPairedReads(features: ChainData): boolean;

package/dist/LinearReadArcsDisplay/util.js

@@ -1,11 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.hasPairedReads = hasPairedReads;
-function hasPairedReads(features) {
-    for (const f of features.chains.values()) {
-        if (f[0].flags & 1) {
-            return true;
-        }
-    }
-    return false;
-}

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,105 +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 jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
-const util_1 = require("@jbrowse/core/util");
-const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
-const mobx_react_1 = require("mobx-react");
-const BaseDisplayComponent_1 = __importDefault(require("../../shared/components/BaseDisplayComponent"));
-const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
-    const view = (0, util_1.getContainingView)(model);
-    const width = Math.round(view.dynamicBlocks.totalWidthPx);
-    const height = model.drawCloud ? model.height : model.layoutHeight;
-    const containerRef = (0, react_1.useRef)(null);
-    const [hoveredFeature, setHoveredFeature] = (0, react_1.useState)(null);
-    const [hoveredFeatureData, setHoveredFeatureData] = (0, react_1.useState)(null);
-    const [mousePosition, setMousePosition] = (0, react_1.useState)(null);
-    const flatbushIndex = (0, react_1.useMemo)(() => {
-        return model.featureLayout ? flatbush_1.default.from(model.featureLayout.data) : null;
-    }, [model.featureLayout]);
-    const cb = (0, react_1.useCallback)((ref) => {
-        model.setRef(ref);
-    }, [model, width, height]);
-    const mouseoverCb = (0, react_1.useCallback)((ref) => {
-        model.setMouseoverRef(ref);
-    }, [model, width, height]);
-    const onMouseMove = (0, react_1.useCallback)((event) => {
-        if (!containerRef.current || !flatbushIndex) {
-            setHoveredFeature(null);
-            setHoveredFeatureData(null);
-            setMousePosition(null);
-            return;
-        }
-        const rect = containerRef.current.getBoundingClientRect();
-        const offsetX = event.clientX - rect.left;
-        const offsetY = event.clientY - rect.top;
-        setMousePosition({ x: event.clientX, y: event.clientY });
-        const results = flatbushIndex.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
-        if (results.length > 0) {
-            const featureIndex = results[0];
-            const feature = model.featuresForFlatbush[featureIndex];
-            if (feature) {
-                setHoveredFeature({
-                    x: feature.chainMinX,
-                    y: feature.y1,
-                    width: feature.chainMaxX - feature.chainMinX,
-                    height: feature.y2 - feature.y1,
-                });
-                setHoveredFeatureData(feature.data);
-            }
-            else {
-                setHoveredFeature(null);
-                setHoveredFeatureData(null);
-            }
-        }
-        else {
-            setHoveredFeature(null);
-            setHoveredFeatureData(null);
-        }
-    }, [flatbushIndex, model.featuresForFlatbush]);
-    const onMouseLeave = (0, react_1.useCallback)(() => {
-        setHoveredFeature(null);
-        setHoveredFeatureData(null);
-        setMousePosition(null);
-    }, []);
-    const onClick = (0, react_1.useCallback)((event) => {
-        if (!containerRef.current || !flatbushIndex) {
-            return;
-        }
-        const rect = containerRef.current.getBoundingClientRect();
-        const offsetX = event.clientX - rect.left;
-        const offsetY = event.clientY - rect.top;
-        const results = flatbushIndex.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
-        if (results.length > 0) {
-            const featureIndex = results[0];
-            const feature = model.featuresForFlatbush[featureIndex];
-            if (feature) {
-                model.selectFeature(feature.chain);
-            }
-        }
-    }, [flatbushIndex, model]);
-    return ((0, jsx_runtime_1.jsxs)("div", { ref: containerRef, style: { position: 'relative', width, height }, onMouseMove: onMouseMove, onMouseLeave: onMouseLeave, onClick: onClick, children: [(0, jsx_runtime_1.jsx)("canvas", { "data-testid": model.drawCloud ? 'cloud-canvas' : 'stack-canvas', ref: cb, style: { width, height, position: 'absolute', left: 0, top: 0 }, width: width * 2, height: height * 2 }), (0, jsx_runtime_1.jsx)("canvas", { "data-testid": "cloud-mouseover-canvas", ref: mouseoverCb, style: {
-                    width,
-                    height,
-                    position: 'absolute',
-                    left: 0,
-                    top: 0,
-                    pointerEvents: 'none',
-                }, width: width * 2, height: height * 2 }), hoveredFeature ? ((0, jsx_runtime_1.jsx)("div", { style: {
-                    position: 'absolute',
-                    left: hoveredFeature.x,
-                    top: hoveredFeature.y,
-                    width: hoveredFeature.width,
-                    height: hoveredFeature.height,
-                    backgroundColor: 'rgba(0, 0, 0, 0.2)',
-                    pointerEvents: 'none',
-                } })) : null, hoveredFeatureData && mousePosition ? ((0, jsx_runtime_1.jsx)(BaseTooltip_1.default, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 20 }, placement: "bottom-start", children: (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("strong", { children: hoveredFeatureData.name }) }), (0, jsx_runtime_1.jsxs)("div", { children: [hoveredFeatureData.refName, ":", hoveredFeatureData.start.toLocaleString(), "-", hoveredFeatureData.end.toLocaleString()] }), hoveredFeatureData.tlen !== 0 ? ((0, jsx_runtime_1.jsxs)("div", { children: ["Template length: ", hoveredFeatureData.tlen] })) : null] }) })) : null] }));
-});
-const LinearReadCloudReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
-    return ((0, jsx_runtime_1.jsx)(BaseDisplayComponent_1.default, { model: model, children: (0, jsx_runtime_1.jsx)(Cloud, { model: model }) }));
-});
-exports.default = LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/components/SetFeatureHeightDialog.d.ts

@@ -1,10 +0,0 @@
-declare const SetFeatureHeightDialog: (props: {
-    model: {
-        setFeatureHeight: (arg?: number) => void;
-        setNoSpacing: (arg?: boolean) => void;
-        featureHeightSetting: number;
-        noSpacing?: boolean;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SetFeatureHeightDialog;

package/dist/LinearReadCloudDisplay/components/SetFeatureHeightDialog.js

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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 SetFeatureHeightDialog = (0, mobx_react_1.observer)(function (props) {
-    const { model, handleClose } = props;
-    const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
-    const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
-    const [noSpacing, setNoSpacing] = (0, react_1.useState)(noSpacingSetting);
-    const ok = height !== '' && !Number.isNaN(+height);
-    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set feature height", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
-                        setHeight(event.target.value);
-                    } }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: !!noSpacing, onChange: () => {
-                            setNoSpacing(val => !val);
-                        } }), label: "Remove spacing between features in y-direction?" }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {
-                                model.setFeatureHeight(height !== '' && !Number.isNaN(+height) ? +height : undefined);
-                                model.setNoSpacing(noSpacing);
-                                handleClose();
-                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                                handleClose();
-                            }, children: "Cancel" })] })] }) }));
-});
-exports.default = SetFeatureHeightDialog;

package/dist/LinearReadCloudDisplay/configSchema.d.ts

@@ -1,55 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    featureHeight: {
-        type: string;
-        defaultValue: number;
-    };
-    colorBy: {
-        type: string;
-        defaultValue: {
-            type: string;
-        };
-    };
-    filterBy: {
-        type: string;
-        defaultValue: {
-            flagInclude: number;
-            flagExclude: number;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
-export default configSchemaF;