@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/shared/SharedVariantMixin.d.ts

@@ -1,325 +0,0 @@
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-export default function SharedVariantMixin(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>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        stopToken: string | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement | undefined;
-        features: Map<string, Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: {
-                error?: unknown;
-                reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
-                reactElement?: React.ReactElement;
-            };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
-        setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: 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">>;
-} & {
-    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    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;
-} & {
-    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;
-} & {
-    mouseoverExtraInformation: string | undefined;
-    featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | Feature;
-} & {
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
-    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
-} & {
-    readonly renderDelay: number;
-    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
-    readonly selectedFeatureId: string | undefined;
-    copyInfoToClipboard(feature: Feature): void;
-} & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
-    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]>;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | undefined;
-    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | undefined;
-} & {
-    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
-    navToFeature(feature: Feature): void;
-    clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string): void;
-    setContextMenuFeature(feature?: Feature): void;
-    setMouseoverExtraInformation(extra?: string): void;
-} & {
-    reload(): Promise<void>;
-} & {
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
-} & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
-    afterAttach(): void;
-} & {
-    message: undefined | string;
-} & {
-    selectFeature(feature: Feature): void;
-    setRendererType(val: string): void;
-} & {
-    readonly adapterTypeName: any;
-    readonly rendererTypeNameSimple: any;
-    readonly filters: undefined;
-} & {
-    readonly adapterCapabilities: string[];
-} & {
-    reload(): Promise<void>;
-}, {
-    type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    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>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        stopToken: string | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement | undefined;
-        features: Map<string, Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: {
-                error?: unknown;
-                reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
-                reactElement?: React.ReactElement;
-            };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
-        setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: 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">>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    id: string;
-    type: string;
-    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    rpcDriverName: string | undefined;
-    heightPreConfig: number | undefined;
-    userBpPerPxLimit: number | undefined;
-    userByteSizeLimit: number | undefined;
-} & import("mobx-state-tree")._NotCustomized>;

package/dist/shared/SharedVariantMixin.js

@@ -1,58 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SharedVariantMixin;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function SharedVariantMixin(configSchema) {
-    return mobx_state_tree_1.types
-        .compose(plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        selectedRendering: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
-        summaryScoreMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        rendererTypeNameState: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-    }))
-        .volatile(() => ({
-        message: undefined,
-    }))
-        .actions(self => ({
-        selectFeature(feature) {
-            const session = (0, util_1.getSession)(self);
-            if ((0, util_1.isSelectionContainer)(session)) {
-                session.setSelection(feature);
-            }
-        },
-        setRendererType(val) {
-            self.rendererTypeNameState = val;
-        },
-    }))
-        .views(self => ({
-        get adapterTypeName() {
-            return self.adapterConfig.type;
-        },
-        get rendererTypeNameSimple() {
-            var _a;
-            return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'defaultRendering');
-        },
-        get filters() {
-            return undefined;
-        },
-    }))
-        .views(self => ({
-        get adapterCapabilities() {
-            const type = self.adapterTypeName;
-            const { pluginManager } = (0, util_1.getEnv)(self);
-            return pluginManager.getAdapterType(type).adapterCapabilities;
-        },
-    }))
-        .actions(self => {
-        const { reload: superReload } = self;
-        return {
-            async reload() {
-                self.setError();
-                superReload();
-            },
-        };
-    });
-}

package/dist/shared/components/AddFiltersDialog.d.ts

@@ -1,9 +0,0 @@
-declare const AddFiltersDialog: ({ model, handleClose, }: {
-    model: {
-        jexlFilters?: string[];
-        activeFilters: string[];
-        setJexlFilters: (arg?: string[]) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AddFiltersDialog;

package/dist/shared/components/AddFiltersDialog.js

@@ -1,61 +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 jexlStrings_1 = require("@jbrowse/core/util/jexlStrings");
-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)()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    error: {
-        color: 'red',
-        fontSize: '0.8em',
-    },
-});
-function checkJexl(code) {
-    (0, jexlStrings_1.stringToJexlExpression)(code);
-}
-const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const { activeFilters } = model;
-    const [data, setData] = (0, react_1.useState)(activeFilters.join('\n'));
-    const [error, setError] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        try {
-            data
-                .split('\n')
-                .map(line => line.trim())
-                .filter(line => !!line)
-                .map(line => {
-                checkJexl(line.trim());
-            });
-            setError(undefined);
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }, [data]);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] })] }), error ? (0, jsx_runtime_1.jsx)("p", { className: classes.error, children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
-                            setData(event.target.value);
-                        }, slotProps: {
-                            input: {
-                                classes: {
-                                    input: classes.textAreaFont,
-                                },
-                            },
-                        } })] }), (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: !!error, onClick: () => {
-                            model.setJexlFilters(data.split('\n'));
-                            handleClose();
-                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = AddFiltersDialog;

package/dist/shared/components/MAFFilterDialog.d.ts

@@ -1,8 +0,0 @@
-declare const MAFFilterDialog: ({ model, handleClose, }: {
-    model: {
-        minorAlleleFrequencyFilter?: number;
-        setMafFilter: (arg: number) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default MAFFilterDialog;

package/dist/shared/components/MAFFilterDialog.js

@@ -1,28 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-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)()({
-    root: {
-        width: 500,
-    },
-});
-const MAFFilterDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    const { minorAlleleFrequencyFilter = '' } = model;
-    const { classes } = useStyles();
-    const [maf, setMaf] = (0, react_1.useState)(`${minorAlleleFrequencyFilter}`);
-    return ((0, jsx_runtime_1.jsx)(material_1.Dialog, { open: true, onClose: handleClose, title: "Set minor allele frequency (MAF)", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.root, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Set minor allele frequency cutoff track. This will filter out rare variants that might not contribute to meaningful large scale patterns" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: maf, autoFocus: true, placeholder: "Enter MAF", onChange: event => {
-                        setMaf(event.target.value);
-                    } }), (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, onClick: () => {
-                                if (!Number.isNaN(+maf)) {
-                                    model.setMafFilter(+maf);
-                                }
-                                handleClose();
-                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                                handleClose();
-                            }, children: "Cancel" })] })] }) }));
-});
-exports.default = MAFFilterDialog;

package/dist/shared/components/MultiVariantBaseDisplayComponent.d.ts

@@ -1,5 +0,0 @@
-import type { MultiVariantBaseModel } from '../MultiVariantBaseModel';
-declare const MultiVariantBaseDisplayComponent: (props: {
-    model: MultiVariantBaseModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default MultiVariantBaseDisplayComponent;

package/dist/shared/components/MultiVariantBaseDisplayComponent.js

@@ -1,29 +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 plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_react_1 = require("mobx-react");
-const MultiVariantCrosshairs_1 = __importDefault(require("./MultiVariantCrosshairs"));
-const MultiVariantLegendBar_1 = __importDefault(require("./MultiVariantLegendBar"));
-const MultiVariantBaseDisplayComponent = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const ref = (0, react_1.useRef)(null);
-    const [mouseY, setMouseY] = (0, react_1.useState)();
-    const [mouseX, setMouseX] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, onMouseMove: event => {
-            var _a;
-            const rect = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect();
-            const top = (rect === null || rect === void 0 ? void 0 : rect.top) || 0;
-            const left = (rect === null || rect === void 0 ? void 0 : rect.left) || 0;
-            setMouseY(event.clientY - top);
-            setMouseX(event.clientX - left);
-        }, onMouseLeave: () => {
-            setMouseY(undefined);
-            setMouseX(undefined);
-        }, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(MultiVariantLegendBar_1.default, { model: model }), mouseX && mouseY ? ((0, jsx_runtime_1.jsx)(MultiVariantCrosshairs_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
-});
-exports.default = MultiVariantBaseDisplayComponent;

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialog.d.ts

@@ -1,6 +0,0 @@
-import type { ReducedModel } from './types';
-declare const ClusterDialog: ({ model, handleClose, }: {
-    model: ReducedModel;
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialog;

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialog.js

@@ -1,29 +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 ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const ClusterDialogAuto_1 = __importDefault(require("./ClusterDialogAuto"));
-const ClusterDialogManual_1 = __importDefault(require("./ClusterDialogManual"));
-function Header({ activeMode, setActiveMode, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { style: { marginBottom: 30 }, children: "This procedure will cluster the visible genotype data using hierarchical clustering" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                    auto: ((0, jsx_runtime_1.jsx)("div", { children: "Run in-app clustering (slower, particularly for large numbers of samples, uses JS implementation of hclust)" })),
-                    manual: ((0, jsx_runtime_1.jsx)("div", { children: "Download R script to run clustering (faster, uses R implementation of hclust)" })),
-                }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: activeMode === key, onChange: () => {
-                            setActiveMode(key);
-                        } }), label: val }, key))) })] }));
-}
-const ClusterDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    const [activeMode, setActiveMode] = (0, react_1.useState)('auto');
-    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Cluster by genotype", onClose: (_, reason) => {
-            if (reason !== 'backdropClick') {
-                handleClose();
-            }
-        }, children: activeMode === 'auto' ? ((0, jsx_runtime_1.jsx)(ClusterDialogAuto_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : ((0, jsx_runtime_1.jsx)(ClusterDialogManual_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
-});
-exports.default = ClusterDialog;

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.d.ts

@@ -1,7 +0,0 @@
-import type { ReducedModel } from './types';
-declare const ClusterDialogAuto: ({ model, children, handleClose, }: {
-    model: ReducedModel;
-    children: React.ReactNode;
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialogAuto;

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.js

@@ -1,74 +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 util_1 = require("@jbrowse/core/util");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const ClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children, handleClose, }) {
-    const [progress, setProgress] = (0, react_1.useState)('');
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const [error, setError] = (0, react_1.useState)();
-    const [stopToken, setStopToken] = (0, react_1.useState)('');
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)("div", { children: [loading ? ((0, jsx_runtime_1.jsxs)("div", { style: { padding: 50 }, children: [(0, jsx_runtime_1.jsx)("span", { children: progress || 'Loading...' }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                                            (0, stopToken_1.stopStopToken)(stopToken);
-                                        }, children: "Stop" })] })) : null, error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null] })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", disabled: loading, onClick: async () => {
-                            try {
-                                setError(undefined);
-                                setProgress('Initializing');
-                                setLoading(true);
-                                const view = (0, util_1.getContainingView)(model);
-                                if (!view.initialized) {
-                                    return;
-                                }
-                                const { rpcManager } = (0, util_1.getSession)(model);
-                                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, lengthCutoffFilter, adapterConfig, } = model;
-                                if (sourcesWithoutLayout) {
-                                    const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                                    const stopToken = (0, stopToken_1.createStopToken)();
-                                    setStopToken(stopToken);
-                                    const ret = (await rpcManager.call(sessionId, 'MultiVariantClusterGenotypeMatrix', {
-                                        regions: view.dynamicBlocks.contentBlocks,
-                                        sources: sourcesWithoutLayout,
-                                        minorAlleleFrequencyFilter,
-                                        lengthCutoffFilter,
-                                        sessionId,
-                                        adapterConfig,
-                                        stopToken,
-                                        statusCallback: (arg) => {
-                                            setProgress(arg);
-                                        },
-                                    }));
-                                    model.setLayout(ret.order.map(idx => {
-                                        const ret = sourcesWithoutLayout[idx];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                handleClose();
-                            }
-                            catch (e) {
-                                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                                    console.error(e);
-                                    setError(e);
-                                }
-                            }
-                            finally {
-                                setLoading(false);
-                                setProgress('');
-                                setStopToken('');
-                            }
-                        }, children: "Run clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                            if (stopToken) {
-                                (0, stopToken_1.stopStopToken)(stopToken);
-                            }
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = ClusterDialogAuto;