@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/dist/shared/RowPalettizer.js

@@ -0,0 +1,38 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = RowPalettizer;
+const react_1 = __importDefault(require("react"));
+const colors_1 = require("@jbrowse/core/ui/colors");
+const material_1 = require("@mui/material");
+const util_1 = require("../util");
+function RowPalettizer({ setCurrLayout, currLayout, }) {
+    var _a;
+    return (react_1.default.createElement("div", null, Object.keys((_a = currLayout[0]) !== null && _a !== void 0 ? _a : [])
+        .filter(f => f !== 'name' && f !== 'color')
+        .map(r => {
+        return (react_1.default.createElement(material_1.Button, { key: r, onClick: () => {
+                const map = new Map();
+                for (const row of currLayout) {
+                    const val = map.get(row[r]);
+                    if (!val) {
+                        map.set(row[r], 1);
+                    }
+                    else {
+                        map.set(row[r], val + 1);
+                    }
+                }
+                const ret = Object.fromEntries([...map.entries()]
+                    .sort((a, b) => a[1] - b[1])
+                    .map((r, idx) => [r[0], colors_1.set1[idx] || (0, util_1.randomColor)(r[0])]));
+                setCurrLayout(currLayout.map(row => ({
+                    ...row,
+                    color: ret[row[r]],
+                })));
+            } },
+            "Palettize ",
+            r));
+    })));
+}

package/dist/shared/SetColorDialog.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import { type Source } from '../util';
+interface ReducedModel {
+    sources?: Source[];
+    setLayout: (s: Source[]) => void;
+    clearLayout: () => void;
+}
+export default function SetColorDialog({ model, handleClose, }: {
+    model: ReducedModel;
+    handleClose: () => void;
+}): React.JSX.Element;
+export {};

package/dist/shared/SetColorDialog.js

@@ -0,0 +1,94 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SetColorDialog;
+const react_1 = __importStar(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const DraggableDialog_1 = __importDefault(require("./DraggableDialog"));
+const SourcesGrid_1 = __importDefault(require("./SourcesGrid"));
+const BulkEditPanel_1 = __importDefault(require("./BulkEditPanel"));
+const RowPalettizer_1 = __importDefault(require("./RowPalettizer"));
+const useStyles = (0, mui_1.makeStyles)()({
+    content: {
+        minWidth: 800,
+    },
+    fr: {
+        float: 'right',
+    },
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+function SetColorDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const { sources } = model;
+    const [showBulkEditor, setShowBulkEditor] = (0, react_1.useState)(false);
+    const [currLayout, setCurrLayout] = (0, react_1.useState)(sources || []);
+    const [showTips, setShowTips] = (0, util_1.useLocalStorage)('multivariant-showTips', false);
+    return (react_1.default.createElement(DraggableDialog_1.default, { open: true, onClose: handleClose, maxWidth: "xl", title: "Multi-variant color/arrangement editor" },
+        react_1.default.createElement(material_1.DialogContent, { className: classes.content },
+            react_1.default.createElement("div", { className: classes.fr },
+                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                        setShowTips(!showTips);
+                    } }, showTips ? 'Hide tips' : 'Show tips'),
+                react_1.default.createElement(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
+                        setShowBulkEditor(!showBulkEditor);
+                    } }, showBulkEditor ? 'Hide bulk row editor' : 'Show Bulk row editor')),
+            react_1.default.createElement("br", null),
+            showTips ? react_1.default.createElement(HelpfulTips, null) : null,
+            showBulkEditor ? (react_1.default.createElement(BulkEditPanel_1.default, { currLayout: currLayout, setCurrLayout: setCurrLayout })) : null,
+            react_1.default.createElement(RowPalettizer_1.default, { currLayout: currLayout, setCurrLayout: setCurrLayout }),
+            react_1.default.createElement(SourcesGrid_1.default, { rows: currLayout, onChange: setCurrLayout, showTips: showTips })),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { variant: "contained", type: "submit", color: "inherit", onClick: () => {
+                    model.clearLayout();
+                    setCurrLayout(model.sources || []);
+                } }, "Clear custom settings"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                    setCurrLayout([...(model.sources || [])]);
+                } }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: () => {
+                    model.setLayout(currLayout);
+                    handleClose();
+                } }, "Submit"))));
+}
+function HelpfulTips() {
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        "Helpful tips",
+        react_1.default.createElement("ul", null,
+            react_1.default.createElement("li", null, "You can select rows in the table with the checkboxes"),
+            react_1.default.createElement("li", null, "Multi-select is enabled with shift-click and control-click"),
+            react_1.default.createElement("li", null, "The \"Move selected items up/down\" can re-arrange subtracks"),
+            react_1.default.createElement("li", null, "Sorting the data grid itself can also re-arrange subtracks"),
+            react_1.default.createElement("li", null, "Changes are applied when you hit Submit"),
+            react_1.default.createElement("li", null, "You can click and drag the dialog box to move it on the screen"),
+            react_1.default.createElement("li", null, "Columns in the table can be hidden using a vertical '...' menu on the right side of each column"))));
+}

package/dist/shared/SetMinMaxDialog.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+export default function SetMinMaxDialog(props: {
+    model: {
+        minScore: number;
+        maxScore: number;
+        scaleType: string;
+        setMinScore: (arg?: number) => void;
+        setMaxScore: (arg?: number) => void;
+    };
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/shared/SetMinMaxDialog.js

@@ -0,0 +1,56 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SetMinMaxDialog;
+const react_1 = __importStar(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+function SetMinMaxDialog(props) {
+    const { model, handleClose } = props;
+    const { minScore, maxScore, scaleType } = model;
+    const [min, setMin] = (0, react_1.useState)(`${minScore !== Number.MIN_VALUE ? minScore : ''}`);
+    const [max, setMax] = (0, react_1.useState)(`${maxScore !== Number.MAX_VALUE ? maxScore : ''}`);
+    const ok = min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
+        ? +max > +min
+        : true;
+    const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track" },
+        react_1.default.createElement(material_1.DialogContent, null,
+            react_1.default.createElement(material_1.Typography, null, "Enter min/max score: "),
+            !ok ? (react_1.default.createElement(material_1.Typography, { color: "error" }, "Max is greater than or equal to min")) : null,
+            !logOk ? (react_1.default.createElement(material_1.Typography, { color: "error" }, "Min score should be greater than 0 for log scale")) : null,
+            react_1.default.createElement(material_1.TextField, { value: min, onChange: event => {
+                    setMin(event.target.value);
+                }, placeholder: "Enter min score" }),
+            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
+                    setMax(event.target.value);
+                }, placeholder: "Enter max score" })),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
+                    model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
+                    model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                    handleClose();
+                } }, "Submit"))));
+}

package/dist/shared/SharedVariantConfigSchema.d.ts

@@ -0,0 +1,66 @@
+export default function sharedVariantConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    minimalTicks: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, 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>>;

package/dist/shared/SharedVariantConfigSchema.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = sharedVariantConfigFactory;
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function sharedVariantConfigFactory() {
+    return (0, configuration_1.ConfigurationSchema)('SharedVariantDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: mobx_state_tree_1.types.enumeration('Autoscale type', [
+                'global',
+                'local',
+                'globalsd',
+                'localsd',
+                'zscore',
+            ]),
+            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
+        },
+        minimalTicks: {
+            type: 'boolean',
+            defaultValue: false,
+            description: 'use the minimal amount of ticks',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        numStdDev: {
+            type: 'number',
+            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
+            defaultValue: 3,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+    }, {
+        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
+}

package/dist/shared/SharedVariantMixin.d.ts

@@ -0,0 +1,309 @@
+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.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.Element | null;
+} & {
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
+} & {
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+    readonly selectedFeatureId: string | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | 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;
+} & {
+    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.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.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, {
+    type: string;
+    id: 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>;