@jbrowse/plugin-linear-genome-view 2.8.0 → 2.10.0

package/dist/index.js

@@ -26,9 +26,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.SVGRuler = exports.totalHeight = exports.SVGTracks = exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.TooLargeMessage = exports.FeatureDensityMixin = exports.TrackHeightMixin = exports.BaseLinearDisplayComponent = exports.BlockMsg = exports.BaseLinearDisplay = exports.baseLinearDisplayConfigSchema = exports.linearBareDisplayConfigSchemaFactory = void 0;
+exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.totalHeight = exports.SVGRuler = exports.SVGTracks = exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.TooLargeMessage = exports.FeatureDensityMixin = exports.TrackHeightMixin = exports.BaseLinearDisplayComponent = exports.BlockMsg = exports.BaseLinearDisplay = exports.baseLinearDisplayConfigSchema = exports.linearBareDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
 // icons
 const LineStyle_1 = __importDefault(require("@mui/icons-material/LineStyle"));
 // locals
@@ -39,8 +41,6 @@ const LinearBasicDisplay_1 = __importDefault(require("./LinearBasicDisplay"));
 const FeatureTrack_1 = __importDefault(require("./FeatureTrack"));
 const BasicTrack_1 = __importDefault(require("./BasicTrack"));
 const LaunchLinearGenomeView_1 = __importDefault(require("./LaunchLinearGenomeView"));
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
 class LinearGenomeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -108,8 +108,9 @@ Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function ()
 var SVGLinearGenomeView_1 = require("./LinearGenomeView/svgcomponents/SVGLinearGenomeView");
 Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return SVGLinearGenomeView_1.renderToSvg; } });
 Object.defineProperty(exports, "SVGTracks", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGTracks; } });
-Object.defineProperty(exports, "totalHeight", { enumerable: true, get: function () { return SVGLinearGenomeView_1.totalHeight; } });
 Object.defineProperty(exports, "SVGRuler", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGRuler; } });
+var util_2 = require("./LinearGenomeView/svgcomponents/util");
+Object.defineProperty(exports, "totalHeight", { enumerable: true, get: function () { return util_2.totalHeight; } });
 var LinearBasicDisplay_2 = require("./LinearBasicDisplay");
 Object.defineProperty(exports, "linearBasicDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBasicDisplay_2.configSchema; } });
 Object.defineProperty(exports, "linearBasicDisplayModelFactory", { enumerable: true, get: function () { return LinearBasicDisplay_2.modelFactory; } });

package/dist/searchUtils.d.ts

@@ -0,0 +1,26 @@
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import { TextSearchManager } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from './LinearGenomeView';
+export declare function navToOption({ option, model, assemblyName, }: {
+    model: LinearGenomeViewModel;
+    option: BaseResult;
+    assemblyName: string;
+}): Promise<void>;
+export declare function handleSelectedRegion({ input, model, assembly, }: {
+    input: string;
+    model: LinearGenomeViewModel;
+    assembly: Assembly;
+}): Promise<void>;
+export declare function checkRef(str: string, allRefs: string[]): boolean;
+export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    queryString: string;
+    searchScope: SearchScope;
+    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    searchType?: SearchType;
+    textSearchManager?: TextSearchManager;
+    assembly?: Assembly;
+}): Promise<BaseResult[]>;
+export declare function splitLast(str: string, split: string): [string, string];

package/dist/searchUtils.js

@@ -0,0 +1,90 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.splitLast = exports.fetchResults = exports.checkRef = exports.handleSelectedRegion = exports.navToOption = void 0;
+const util_1 = require("@jbrowse/core/util");
+const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+const util_2 = require("@jbrowse/core/util");
+async function navToOption({ option, model, assemblyName, }) {
+    const location = option.getLocation();
+    const trackId = option.getTrackId();
+    if (location) {
+        await model.navToLocString(location, assemblyName);
+        if (trackId) {
+            model.showTrack(trackId);
+        }
+    }
+}
+exports.navToOption = navToOption;
+// gets a string as input, or use stored option results from previous query,
+// then re-query and
+// 1) if it has multiple results: pop a dialog
+// 2) if it's a single result navigate to it
+// 3) else assume it's a locstring and navigate to it
+async function handleSelectedRegion({ input, model, assembly, }) {
+    const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
+    const assemblyName = assembly.name;
+    if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
+        await model.navToLocString(input, assembly.name);
+    }
+    else {
+        const searchScope = model.searchScope(assemblyName);
+        const { textSearchManager } = (0, util_1.getSession)(model);
+        const results = await fetchResults({
+            queryString: input,
+            searchType: 'exact',
+            searchScope,
+            rankSearchResults: model.rankSearchResults,
+            textSearchManager,
+            assembly,
+        });
+        if (results.length > 1) {
+            model.setSearchResults(results, input.toLowerCase(), assemblyName);
+        }
+        else if (results.length === 1) {
+            await navToOption({
+                option: results[0],
+                model,
+                assemblyName,
+            });
+        }
+        else {
+            await model.navToLocString(input, assemblyName);
+        }
+    }
+}
+exports.handleSelectedRegion = handleSelectedRegion;
+function checkRef(str, allRefs) {
+    const [ref, rest] = splitLast(str, ':');
+    return (allRefs.includes(str) ||
+        (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10))));
+}
+exports.checkRef = checkRef;
+async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
+    var _a;
+    if (!textSearchManager) {
+        console.warn('No text search manager');
+    }
+    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+        queryString,
+        searchType,
+    }, searchScope, rankSearchResults));
+    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResults_1.default({ label: r }));
+    return (0, util_2.dedupe)([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+}
+exports.fetchResults = fetchResults;
+// splits on the last instance of a character
+function splitLast(str, split) {
+    const lastIndex = str.lastIndexOf(split);
+    if (lastIndex === -1) {
+        return [str, ''];
+    }
+    else {
+        const before = str.slice(0, lastIndex);
+        const after = str.slice(lastIndex + 1);
+        return [before, after];
+    }
+}
+exports.splitLast = splitLast;

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -1,10 +1,10 @@
-import React, { useState, useMemo } from 'react';
+import React from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { SanitizedHTML } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { Portal, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { usePopper } from 'react-popper';
+import { useClientPoint, useFloating, useInteractions, } from '@floating-ui/react';
 function round(value) {
     return Math.round(value * 1e5) / 1e5;
 }
@@ -27,39 +27,27 @@ const useStyles = makeStyles()(theme => ({
 const TooltipContents = React.forwardRef(function TooltipContents2({ message }, ref) {
     return (React.createElement("div", { ref: ref }, React.isValidElement(message) ? (message) : message ? (React.createElement(SanitizedHTML, { html: String(message) })) : null));
 });
-const Tooltip = observer(({ model, clientMouseCoord, }) => {
+const Tooltip = observer(function ({ model, clientMouseCoord, }) {
     var _a, _b;
     const { theme, classes } = useStyles();
     const { featureUnderMouse } = model;
-    const [width, setWidth] = useState(0);
-    const [popperElt, setPopperElt] = useState(null);
-    // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-    const virtElement = useMemo(() => ({
-        getBoundingClientRect: () => {
-            const x = clientMouseCoord[0] + width / 2 + 20;
-            const y = clientMouseCoord[1];
-            return {
-                top: y,
-                left: x,
-                bottom: y,
-                right: x,
-                width: 0,
-                height: 0,
-                x,
-                y,
-                toJSON() { },
-            };
-        },
-    }), [clientMouseCoord, width]);
-    const { styles, attributes } = usePopper(virtElement, popperElt);
+    const x = clientMouseCoord[0] + 15;
+    const y = clientMouseCoord[1];
+    const { refs, floatingStyles, context } = useFloating({
+        placement: 'right',
+    });
+    const clientPoint = useClientPoint(context, { x, y });
+    const { getFloatingProps } = useInteractions([clientPoint]);
     const contents = featureUnderMouse
         ? getConf(model, 'mouseover', { feature: featureUnderMouse })
         : undefined;
     const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return featureUnderMouse && contents ? (React.createElement(Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
-        React.createElement("div", { ref: setPopperElt, className: classes.tooltip, 
-            // zIndex needed to go over widget drawer
-            style: { ...styles.popper, zIndex: 100000 }, ...attributes.popper },
-            React.createElement(TooltipContents, { ref: elt => setWidth((elt === null || elt === void 0 ? void 0 : elt.getBoundingClientRect().width) || 0), message: contents })))) : null;
+        React.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
+                ...floatingStyles,
+                zIndex: 100000,
+                pointerEvents: 'none',
+            }, ...getFloatingProps() },
+            React.createElement(TooltipContents, { message: contents })))) : null;
 });
 export default Tooltip;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -69,11 +69,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>; /**
-             * #getter
-             * a CompositeMap of `featureId -> feature obj` that
-             * just looks in all the block data for that feature
-             */
+            features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -132,9 +128,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined; /**
-         * #property
-         */
+        blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -142,9 +136,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -361,11 +353,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>; /**
-             * #getter
-             * a CompositeMap of `featureId -> feature obj` that
-             * just looks in all the block data for that feature
-             */
+            features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -15,7 +15,14 @@ import FeatureDensityMixin from './FeatureDensityMixin';
 /**
  * #stateModel BaseLinearDisplay
  * #category display
- * extends `BaseDisplay`
+ *
+ * BaseLinearDisplay is used as the basis for many linear genome view tracks.
+ * It is block based, and can use 'static blocks' or 'dynamic blocks'
+ *
+ * extends
+ * - [BaseDisplay](../basedisplay)
+ * - [TrackHeightMixin](../trackheightmixin)
+ * - [FeatureDensityMixin](../featuredensitymixin)
  */
 function stateModelFactory() {
     return types

package/esm/BasicTrack/configSchema.d.ts

@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {

package/esm/FeatureTrack/configSchema.d.ts

@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {

package/esm/LaunchLinearGenomeView/index.js

@@ -1,4 +1,5 @@
 import { when } from '@jbrowse/core/util';
+import { handleSelectedRegion } from '..//searchUtils';
 export default (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
@@ -14,21 +15,9 @@ export default (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
-            await view.navToLocString(loc, assembly);
+            await handleSelectedRegion({ input: loc, model: view, assembly: asm });
             const idsNotFound = [];
-            tracks.forEach(track => {
-                try {
-                    view.showTrack(track);
-                }
-                catch (e) {
-                    if (`${e}`.match('Could not resolve identifier')) {
-                        idsNotFound.push(track);
-                    }
-                    else {
-                        throw e;
-                    }
-                }
-            });
+            tracks.forEach(track => tryTrack(view, track, idsNotFound));
             if (idsNotFound.length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }
@@ -39,3 +28,16 @@ export default (pluginManager) => {
         }
     });
 };
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}

package/esm/LinearBareDisplay/model.d.ts

@@ -3,7 +3,8 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
  * #stateModel LinearBareDisplay
  * #category display
- * extends `BaseLinearDisplay`
+ * extends
+ * - [BaseLinearDisplay](../baselineardisplay)
  */
 export declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -76,9 +77,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #getter
-         */
+        };
         mouseover: {
             type: string;
             description: string;
@@ -98,9 +97,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 }, {
     rendererTypeName: string;
     error: unknown;
-    message: string | undefined; /**
-     * #property
-     */
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -160,7 +157,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly height: number;
 } & {
-    setScrollTop(scrollTop: number): void;
+    setScrollTop(scrollTop: number): void; /**
+     * #method
+     */
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
@@ -303,9 +302,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #getter
-         */
+        };
         mouseover: {
             type: string;
             description: string;

package/esm/LinearBareDisplay/model.js

@@ -5,7 +5,8 @@ import { BaseLinearDisplay } from '../BaseLinearDisplay';
 /**
  * #stateModel LinearBareDisplay
  * #category display
- * extends `BaseLinearDisplay`
+ * extends
+ * - [BaseLinearDisplay](../baselineardisplay)
  */
 export function stateModelFactory(configSchema) {
     return types

package/esm/LinearBasicDisplay/model.d.ts

@@ -7,6 +7,9 @@ import { Instance } from 'mobx-state-tree';
  * #category display
  * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
  * etc.
+ *
+ * extends
+ * - [BaseLinearDisplay](../baselineardisplay)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -34,7 +37,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        renderInProgress: AbortController | undefined; /**
+         * #property
+         */
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -52,9 +57,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #method
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
@@ -81,15 +84,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #property
-         */
+        };
         mouseover: {
             type: string;
             description: string;
-            defaultValue: string; /**
-             * #property
-             */
+            defaultValue: string;
             contextVariable: string[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
@@ -127,9 +126,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined; /**
-             * #property
-             */
+            rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -160,13 +157,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: string; /**
-             * #action
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
+    /**
+     * #action
+     */
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
@@ -195,10 +193,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly featureDensityStatsReady: boolean; /**
+    /**
      * #getter
      */
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     afterAttach(): void;
@@ -219,9 +218,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly blockType: "dynamicBlocks" | "staticBlocks"; /**
-     * #getter
-     */
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -278,7 +275,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: unknown): any; /**
+         * #property
+         */
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**
@@ -305,7 +304,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         config: {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: unknown): any;
+            setSubschema(slotName: string, data: unknown): any; /**
+             * #property
+             */
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     };
     /**
@@ -340,7 +341,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        renderInProgress: AbortController | undefined; /**
+         * #property
+         */
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -358,9 +361,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #method
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
@@ -387,15 +388,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             defaultValue: number;
             description: string;
-        }; /**
-         * #property
-         */
+        };
         mouseover: {
             type: string;
             description: string;
-            defaultValue: string; /**
-             * #property
-             */
+            defaultValue: string;
             contextVariable: string[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/esm/LinearBasicDisplay/model.js

@@ -12,6 +12,9 @@ const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
  * #category display
  * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
  * etc.
+ *
+ * extends
+ * - [BaseLinearDisplay](../baselineardisplay)
  */
 function stateModelFactory(configSchema) {
     return types

package/esm/LinearGenomeView/components/CenterLine.js

@@ -5,7 +5,7 @@ const useStyles = makeStyles()(theme => ({
     centerLineContainer: {
         background: 'transparent',
         height: '100%',
-        zIndex: 5,
+        zIndex: 5, // above the track but under menu
         position: 'absolute',
         border: `1px ${theme.palette.action.active} dashed`,
         borderTop: 'none',

package/esm/LinearGenomeView/components/Cytobands.d.ts

@@ -53,11 +53,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -109,11 +115,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;