@jbrowse/plugin-alignments 2.12.0 → 2.12.1

package/dist/AlignmentsFeatureDetail/Flags.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = AlignmentFlags;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
@@ -41,4 +42,3 @@ function AlignmentFlags(props) {
             return (react_1.default.createElement(material_1.FormControlLabel, { key: key, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
         }))));
 }
-exports.default = AlignmentFlags;

package/dist/AlignmentsFeatureDetail/Formatter.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = Formatter;
 const react_1 = __importStar(require("react"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 // this 'show more...' used specifically as a formatter on alignments feature
@@ -44,4 +45,3 @@ function Formatter({ value }) {
         react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
         react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`))) : (react_1.default.createElement("div", null, display));
 }
-exports.default = Formatter;

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LaunchBreakpointSplitViewPanel;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
@@ -82,4 +83,3 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
                         (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
         })))) : null;
 }
-exports.default = LaunchBreakpointSplitViewPanel;

package/dist/AlignmentsFeatureDetail/PairLink.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = PairLink;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("./util");
@@ -13,4 +14,3 @@ function PairLink({ locString, model, }) {
             (0, util_1.navToLoc)(locString, model);
         }, href: "#" }, locString));
 }
-exports.default = PairLink;

package/dist/AlignmentsFeatureDetail/SuppAlignments.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SuppAlignments;
 const react_1 = __importDefault(require("react"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
@@ -23,4 +24,3 @@ function SuppAlignments(props) {
         react_1.default.createElement(SuppAlignmentsLocStrings_1.default, { model: model, tag: tag }),
         viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }
-exports.default = SuppAlignments;

package/dist/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SuppAlignmentsLocStrings;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 // locals
@@ -34,4 +35,3 @@ function SuppAlignmentsLocStrings({ tag, model, }) {
                     } }, displayString)));
         }))));
 }
-exports.default = SuppAlignmentsLocStrings;

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSAFeatures = void 0;
+exports.getSAFeatures = getSAFeatures;
 const util_1 = require("@jbrowse/core/util");
 // locals
 const MismatchParser_1 = require("../MismatchParser");
@@ -38,4 +38,3 @@ async function getSAFeatures({ view, feature, }) {
     features.sort((a, b) => a.clipPos - b.clipPos);
     return features;
 }
-exports.getSAFeatures = getSAFeatures;

package/dist/AlignmentsFeatureDetail/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = AlignmentFeatureDetailsF;
 const react_1 = require("react");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 const configSchema_1 = require("./configSchema");
@@ -39,4 +40,3 @@ function AlignmentFeatureDetailsF(pluginManager) {
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AlignmentsFeatureDetail')))),
     }));
 }
-exports.default = AlignmentFeatureDetailsF;

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBreakpointSplitView = void 0;
+exports.getBreakpointSplitView = getBreakpointSplitView;
 const util_1 = require("@jbrowse/core/util");
 function getBreakpointSplitView({ f1, f2, view, }) {
     const { assemblyName } = view.displayedRegions[0];
@@ -47,4 +47,3 @@ function getBreakpointSplitView({ f1, f2, view, }) {
         displayName: `breakend split detail`,
     };
 }
-exports.getBreakpointSplitView = getBreakpointSplitView;

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -43,7 +43,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = void 0;
+exports.stateModelFactory = stateModelFactory;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 function stateModelFactory(pluginManager) {
@@ -9,4 +9,3 @@ function stateModelFactory(pluginManager) {
         type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
     }));
 }
-exports.stateModelFactory = stateModelFactory;

package/dist/AlignmentsFeatureDetail/util.js

@@ -1,12 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.navToLoc = exports.getTag = void 0;
+exports.getTag = getTag;
+exports.navToLoc = navToLoc;
 const util_1 = require("@jbrowse/core/util");
 function getTag(tag, feat) {
     var _a;
     return ((_a = feat.tags) === null || _a === void 0 ? void 0 : _a[tag]) || feat[tag];
 }
-exports.getTag = getTag;
 async function navToLoc(locString, model) {
     const session = (0, util_1.getSession)(model);
     const { view } = model;
@@ -23,4 +23,3 @@ async function navToLoc(locString, model) {
         session.notify(`${e}`);
     }
 }
-exports.navToLoc = navToLoc;

package/dist/AlignmentsTrack/configSchemaF.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = configSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 /**
@@ -15,4 +16,3 @@ function configSchemaFactory(pluginManager) {
         baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
     });
 }
-exports.default = configSchemaFactory;

package/dist/AlignmentsTrack/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = register;
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
@@ -23,4 +24,3 @@ function register(pm) {
         return track;
     });
 }
-exports.default = register;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -20,7 +20,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     protected configure(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+        sequenceAdapter?: BaseFeatureDataAdapter;
     }>;
     getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { BamRecord } from '@gmod/bam';
 import BamAdapter from './BamAdapter';

package/dist/BamAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BamAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BamAdapterF(pluginManager) {
@@ -38,4 +39,3 @@ function BamAdapterF(pluginManager) {
         });
     });
 }
-exports.default = BamAdapterF;

package/dist/CramAdapter/CramTestAdapters.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SequenceAdapter = exports.FetchableSmallFasta = exports.parseSmallFasta = void 0;
+exports.SequenceAdapter = exports.FetchableSmallFasta = void 0;
+exports.parseSmallFasta = parseSmallFasta;
 const rxjs_1 = require("rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
@@ -21,7 +22,6 @@ function parseSmallFasta(text) {
         return { id, description, sequence };
     });
 }
-exports.parseSmallFasta = parseSmallFasta;
 class FetchableSmallFasta {
     constructor(filehandle) {
         this.data = filehandle.readFile().then(buffer => {

package/dist/CramAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = CramAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
@@ -39,4 +40,3 @@ function CramAdapterF(pluginManager) {
         });
     });
 }
-exports.default = CramAdapterF;

package/dist/CramAdapter/util.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.readFeaturesToCIGAR = exports.readFeaturesToMismatches = void 0;
+exports.readFeaturesToMismatches = readFeaturesToMismatches;
+exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
 function readFeaturesToMismatches(readFeatures, start, qual) {
     if (!readFeatures) {
         return [];
@@ -116,7 +117,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
     }
     return mismatches.slice(0, j);
 }
-exports.readFeaturesToMismatches = readFeaturesToMismatches;
 function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     let seq = '';
     let cigar = '';
@@ -234,4 +234,3 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     }
     return cigar;
 }
-exports.readFeaturesToCIGAR = readFeaturesToCIGAR;

package/dist/GuessAlignmentsTypes/index.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = GuessAlignmentsTypesF;
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
@@ -53,4 +54,3 @@ function GuessAlignmentsTypesF(pluginManager) {
         };
     });
 }
-exports.default = GuessAlignmentsTypesF;

package/dist/HtsgetBamAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = HtsgetBamAdapterF;
 const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 function HtsgetBamAdapterF(pluginManager) {
@@ -41,4 +42,3 @@ function HtsgetBamAdapterF(pluginManager) {
         });
     });
 }
-exports.default = HtsgetBamAdapterF;

package/dist/LinearAlignmentsDisplay/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearAlignmentsDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 // locals
 const configSchema_1 = __importDefault(require("./models/configSchema"));
@@ -22,4 +23,3 @@ function LinearAlignmentsDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearAlignmentsDisplayF;

package/dist/LinearAlignmentsDisplay/models/alignmentsModel.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LinearAlignmentsDisplayMixin = void 0;
+exports.LinearAlignmentsDisplayMixin = LinearAlignmentsDisplayMixin;
 const mobx_state_tree_1 = require("mobx-state-tree");
 // jbrowse
 const configuration_1 = require("@jbrowse/core/configuration");
@@ -47,4 +47,3 @@ function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
         lowerPanelType: 'LinearPileupDisplay',
     });
 }
-exports.LinearAlignmentsDisplayMixin = LinearAlignmentsDisplayMixin;

package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -25,9 +25,7 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         type: string;
         description: string;
         defaultValue: number;
-    }; /**
-     * #slot
-     */
+    };
     fetchSizeLimit: {
         type: string;
         defaultValue: number;

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = configModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 /**
@@ -33,4 +34,3 @@ function configModelFactory(pm) {
         explicitlyTyped: true,
     });
 }
-exports.default = configModelFactory;

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -37,7 +37,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & 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>>;
@@ -46,8 +46,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -58,28 +58,38 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & 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>>;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import(
+            /**
+             * #action
+             */
+            "mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree" /**
+             * #getter
+             */).ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree" /**
+             * #getter
+             */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import(
+        /**
+         * #getter
+         */
+        "mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
-    trackMenuItems(): MenuItem[]; /**
-     * #getter
-     */
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;

package/dist/LinearAlignmentsDisplay/models/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getLowerPanelDisplays = void 0;
+exports.getLowerPanelDisplays = getLowerPanelDisplays;
 function getLowerPanelDisplays(pluginManager) {
     return (pluginManager
         .getDisplayElements()
@@ -9,4 +9,3 @@ function getLowerPanelDisplays(pluginManager) {
         // @ts-expect-error
         .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
 }
-exports.getLowerPanelDisplays = getLowerPanelDisplays;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { Feature } from '@jbrowse/core/util';
@@ -38,7 +37,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -50,9 +49,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -61,11 +60,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -171,8 +168,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -182,9 +179,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #property
-             */
+            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>;
@@ -199,12 +194,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -217,8 +212,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -229,13 +224,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     afterAttach(): void;
 } & {
-    setCurrStatsBpPerPx(n: number): void; /**
-     * #property
-     */
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): 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 | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -244,8 +237,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     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: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -253,7 +246,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -266,8 +259,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -279,7 +272,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: Feature | undefined;
+    featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
@@ -344,7 +337,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**
@@ -395,8 +394,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 pos: number;
                 refName: number;
                 type: string;
-                tag?: string | undefined;
-            } | undefined;
+                tag?: string;
+            };
         };
     }) => import("react").JSX.Element | null;
     /**
@@ -454,7 +453,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -466,9 +465,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -477,11 +476,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;