@jbrowse/plugin-alignments 2.11.2 → 2.12.1

package/dist/PileupRenderer/renderModifications.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderModifications = void 0;
+exports.renderModifications = renderModifications;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("../util");
@@ -46,4 +46,3 @@ function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWid
         }
     }
 }
-exports.renderModifications = renderModifications;

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseLettering = void 0;
+exports.renderPerBaseLettering = renderPerBaseLettering;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
@@ -43,4 +43,3 @@ function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, cont
         }
     }
 }
-exports.renderPerBaseLettering = renderPerBaseLettering;

package/dist/PileupRenderer/renderPerBaseQuality.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseQuality = void 0;
+exports.renderPerBaseQuality = renderPerBaseQuality;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
@@ -35,4 +35,3 @@ function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
         }
     }
 }
-exports.renderPerBaseQuality = renderPerBaseQuality;

package/dist/PileupRenderer/renderSoftClipping.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSoftClipping = void 0;
+exports.renderSoftClipping = renderSoftClipping;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 // locals
@@ -61,4 +61,3 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
         }
     }
 }
-exports.renderSoftClipping = renderSoftClipping;

package/dist/PileupRenderer/util.js

@@ -1,6 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getCharWidthHeight = exports.shouldDrawIndels = exports.shouldDrawSNPsMuted = exports.getContrastBaseMap = exports.getColorBaseMap = exports.fillRect = void 0;
+exports.fillRect = fillRect;
+exports.getColorBaseMap = getColorBaseMap;
+exports.getContrastBaseMap = getContrastBaseMap;
+exports.shouldDrawSNPsMuted = shouldDrawSNPsMuted;
+exports.shouldDrawIndels = shouldDrawIndels;
+exports.getCharWidthHeight = getCharWidthHeight;
 const util_1 = require("@jbrowse/core/util");
 function fillRect(ctx, l, t, w, h, cw, color) {
     if (l + w < 0 || l > cw) {
@@ -13,7 +18,6 @@ function fillRect(ctx, l, t, w, h, cw, color) {
         ctx.fillRect(l, t, w, h);
     }
 }
-exports.fillRect = fillRect;
 function getColorBaseMap(theme) {
     const { bases } = theme.palette;
     return {
@@ -24,22 +28,18 @@ function getColorBaseMap(theme) {
         deletion: '#808080', // gray
     };
 }
-exports.getColorBaseMap = getColorBaseMap;
 function getContrastBaseMap(theme) {
     return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
         key,
         theme.palette.getContrastText(value),
     ]));
 }
-exports.getContrastBaseMap = getContrastBaseMap;
 function shouldDrawSNPsMuted(type) {
     return ['methylation', 'modifications'].includes(type || '');
 }
-exports.shouldDrawSNPsMuted = shouldDrawSNPsMuted;
 function shouldDrawIndels() {
     return true;
 }
-exports.shouldDrawIndels = shouldDrawIndels;
 // get width and height of chars the height is an approximation: width letter M
 // is approximately the height
 function getCharWidthHeight() {
@@ -47,4 +47,3 @@ function getCharWidthHeight() {
     const charHeight = (0, util_1.measureText)('M') - 2;
     return { charWidth, charHeight };
 }
-exports.getCharWidthHeight = getCharWidthHeight;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = generateCoverageBins;
 const util_1 = require("../util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("@jbrowse/core/util");
@@ -208,4 +209,3 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
     }
     return { bins, skipmap };
 }
-exports.default = generateCoverageBins;

package/dist/SNPCoverageAdapter/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 = SNPCoverageAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function SNPCoverageAdapterF(pluginManager) {
@@ -41,4 +42,3 @@ function SNPCoverageAdapterF(pluginManager) {
         });
     });
 }
-exports.default = SNPCoverageAdapterF;

package/dist/SNPCoverageRenderer/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 configSchema_1 = __importDefault(require("./configSchema"));
 const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
@@ -14,4 +15,3 @@ function register(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = register;

package/dist/shared/afterAttach.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.doAfterAttach = void 0;
+exports.doAfterAttach = doAfterAttach;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("../util");
 const fetchChains_1 = require("./fetchChains");
@@ -40,4 +40,3 @@ function doAfterAttach(self, cb) {
         draw(view);
     }, { delay: 1000 });
 }
-exports.doAfterAttach = doAfterAttach;

package/dist/shared/color.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ColorByModel = exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+exports.ColorByModel = exports.strokeColor = exports.fillColor = void 0;
+exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
+exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
+exports.getPairedOrientationColor = getPairedOrientationColor;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../util");
 exports.fillColor = {
@@ -61,11 +64,9 @@ function getPairedInsertSizeColor(f1, f2, stats) {
     }
     return undefined;
 }
-exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
 function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
     return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
 function getPairedOrientationColor(f) {
     const type = util_1.orientationTypes.fr;
     const type2 = util_1.pairMap[type[f.pair_orientation || '']];
@@ -74,7 +75,6 @@ function getPairedOrientationColor(f) {
         exports.strokeColor[type2] || exports.strokeColor.color_unknown,
     ];
 }
-exports.getPairedOrientationColor = getPairedOrientationColor;
 exports.ColorByModel = mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
     type: mobx_state_tree_1.types.string,
     tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),

package/dist/shared/fetchChains.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchChains = void 0;
+exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
@@ -21,4 +21,3 @@ async function fetchChains(self) {
     self.setChainData(ret);
     self.setLoading(false);
 }
-exports.fetchChains = fetchChains;

package/dist/shared/index.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FilterModel = exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+exports.FilterModel = void 0;
+exports.getUniqueTagValues = getUniqueTagValues;
+exports.getUniqueModificationValues = getUniqueModificationValues;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -17,7 +19,6 @@ async function getUniqueTagValues(self, colorScheme, blocks, opts) {
     });
     return values;
 }
-exports.getUniqueTagValues = getUniqueTagValues;
 async function getUniqueModificationValues(self, adapterConfig, colorScheme, blocks, opts) {
     const { rpcManager } = (0, util_1.getSession)(self);
     const sessionId = (0, tracks_1.getRpcSessionId)(self);
@@ -30,7 +31,6 @@ async function getUniqueModificationValues(self, adapterConfig, colorScheme, blo
     });
     return values;
 }
-exports.getUniqueModificationValues = getUniqueModificationValues;
 exports.FilterModel = mobx_state_tree_1.types.model({
     flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
     flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),

package/dist/shared/renderSvg.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSvg = void 0;
+exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 // stabilize clipid under test for snapshot
@@ -65,4 +65,3 @@ async function renderSvg(self, opts, cb) {
                 dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
     }
 }
-exports.renderSvg = renderSvg;

package/dist/shared/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.hasPairedReads = void 0;
+exports.hasPairedReads = hasPairedReads;
 function hasPairedReads(features) {
     for (const f of features.chains.values()) {
         if (f[0].flags & 1) {
@@ -9,4 +9,3 @@ function hasPairedReads(features) {
     }
     return false;
 }
-exports.hasPairedReads = hasPairedReads;

package/dist/util.d.ts

@@ -17,7 +17,7 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): boolean;
+export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
 export declare const modificationColors: Record<string, string | undefined>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;

package/dist/util.js

@@ -1,6 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.randomColor = exports.createAutorun = exports.modificationColors = exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.pairMap = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
+exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
+exports.getTag = getTag;
+exports.getTagAlt = getTagAlt;
+exports.getColorWGBS = getColorWGBS;
+exports.fetchSequence = fetchSequence;
+exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+exports.createAutorun = createAutorun;
+exports.randomColor = randomColor;
 const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -11,14 +18,12 @@ function getTag(feature, tag) {
     const tags = feature.get('tags');
     return tags !== undefined ? tags[tag] : feature.get(tag);
 }
-exports.getTag = getTag;
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
     var _a;
     return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
-exports.getTagAlt = getTagAlt;
 // orientation definitions from igv.js, see also
 // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 exports.orientationTypes = {
@@ -78,7 +83,6 @@ function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-exports.getColorWGBS = getColorWGBS;
 // fetches region sequence augmenting by +/- 1bp for CpG on either side of
 // requested region
 async function fetchSequence(region, adapter) {
@@ -94,12 +98,10 @@ async function fetchSequence(region, adapter) {
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-exports.fetchSequence = fetchSequence;
 // has to check underlying C-G (aka CpG) on the reference sequence
 function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
 // adapted from IGV
 // https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
 exports.modificationColors = {
@@ -124,8 +126,6 @@ function createAutorun(self, cb, opts) {
         }
     }, opts));
 }
-exports.createAutorun = createAutorun;
 function randomColor() {
     return `hsl(${Math.random() * 200}, 50%, 50%)`;
 }
-exports.randomColor = randomColor;

package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -1,18 +1,11 @@
 import React, { lazy, useEffect, useState } from 'react';
 import { Typography, Link, Tooltip } from '@mui/material';
 import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
-import { makeStyles } from 'tss-react/mui';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getSAFeatures } from './getSAFeatures';
 // lazies
 const BreakendOptionDialog = lazy(() => import('./BreakendOptionDialog'));
-const useStyles = makeStyles()({
-    cursor: {
-        cursor: 'pointer',
-    },
-});
 export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const { classes } = useStyles();
     const session = getSession(model);
     const { view } = model;
     const [res, setRes] = useState();
@@ -47,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
             const [f1, f2] = arg;
             return (React.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
                 React.createElement(Tooltip, { title: "Top panel->Bottom panel" },
-                    React.createElement(Link, { href: "#", className: classes.cursor, onClick: event => {
+                    React.createElement(Link, { href: "#", onClick: event => {
                             event.preventDefault();
                             session.queueDialog(handleClose => [
                                 BreakendOptionDialog,

package/esm/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js

@@ -22,7 +22,7 @@ export default function SuppAlignmentsLocStrings({ tag, model, }) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
             return (React.createElement("li", { key: `${locString}-${index}` },
-                React.createElement(Link, { onClick: async (event) => {
+                React.createElement(Link, { href: "#", onClick: async (event) => {
                         event.preventDefault();
                         // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         navToLoc(locString, model);

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -30,7 +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;
@@ -48,13 +61,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/esm/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/esm/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/esm/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/esm/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;