@jbrowse/core 2.11.2 → 2.12.1

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js

@@ -4,11 +4,57 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+// locals
 const util_1 = require("../util");
-function GenomicSequence({ sequence, upstream, downstream, }) {
+const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
+const GenomicSequence = (0, mobx_react_1.observer)(function ({ sequence, upstream, feature, downstream, model, }) {
+    const { charactersPerRow, showCoordinatesSetting, showCoordinates } = model;
+    let currStart = 0;
+    let upstreamChunk = null;
+    let currRemainder = 0;
+    const strand = feature.strand === -1 ? -1 : 1;
+    const fullGenomicCoordinates = showCoordinatesSetting === 'genomic';
+    const mult = fullGenomicCoordinates ? strand : 1;
+    let coordStart = fullGenomicCoordinates
+        ? strand > 0
+            ? feature.start + 1 - ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
+            : feature.end + ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
+        : 0;
+    if (upstream) {
+        const { segments, remainder } = (0, util_1.splitString)({
+            str: upstream,
+            charactersPerRow,
+            showCoordinates,
+        });
+        upstreamChunk = (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_1.updownstreamColor, start: currStart, coordStart: coordStart, chunks: segments }));
+        currRemainder = remainder;
+        currStart = currStart + upstream.length * mult;
+        coordStart = coordStart + upstream.length * mult;
+    }
+    const { segments, remainder } = (0, util_1.splitString)({
+        str: sequence,
+        charactersPerRow,
+        showCoordinates,
+        currRemainder,
+    });
+    const middleChunk = (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_1.genomeColor, start: currStart, coordStart: coordStart, chunks: segments }));
+    currRemainder = remainder;
+    currStart += sequence.length * mult;
+    coordStart = coordStart + sequence.length * mult;
+    let downstreamChunk = null;
+    if (downstream) {
+        const { segments } = (0, util_1.splitString)({
+            str: downstream,
+            charactersPerRow,
+            currRemainder,
+            showCoordinates,
+        });
+        downstreamChunk = (react_1.default.createElement(SequenceDisplay_1.default, { start: currStart, model: model, chunks: segments, coordStart: coordStart, color: util_1.updownstreamColor }));
+    }
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, upstream)) : null,
-        react_1.default.createElement("span", { style: { background: util_1.genomeColor } }, sequence),
-        downstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, downstream)) : null));
-}
+        upstreamChunk,
+        middleChunk,
+        downstreamChunk));
+});
 exports.default = GenomicSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts

@@ -1,7 +1,10 @@
 import React from 'react';
 import { Feat } from '../../util';
-export default function ProteinSequence({ cds, sequence, codonTable, }: {
+import { SequenceFeatureDetailsModel } from '../model';
+declare const ProteinSequence: ({ cds, sequence, codonTable, model, }: {
     cds: Feat[];
     sequence: string;
     codonTable: Record<string, string>;
-}): React.JSX.Element;
+    model: SequenceFeatureDetailsModel;
+}) => React.JSX.Element;
+export default ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js

@@ -4,15 +4,24 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+// locals
 const util_1 = require("../../util");
 const util_2 = require("../util");
-function ProteinSequence({ cds, sequence, codonTable, }) {
+const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
+const ProteinSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, codonTable, model, }) {
+    const { charactersPerRow, showCoordinates } = model;
     const str = (0, util_1.stitch)(cds, sequence);
     let protein = '';
     for (let i = 0; i < str.length; i += 3) {
         // use & symbol for undefined codon, or partial slice
         protein += codonTable[str.slice(i, i + 3)] || '&';
     }
-    return react_1.default.createElement("span", { style: { background: util_2.proteinColor } }, protein);
-}
+    const { segments } = (0, util_2.splitString)({
+        str: protein,
+        charactersPerRow,
+        showCoordinates,
+    });
+    return (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_2.proteinColor, chunks: segments, start: 0 }));
+});
 exports.default = ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import { SequenceFeatureDetailsModel } from '../model';
+declare const SequenceDisplay: ({ chunks, start, color, strand, coordStart, model, }: {
+    chunks: string[];
+    start: number;
+    coordStart?: number;
+    strand?: number;
+    color?: string;
+    model: SequenceFeatureDetailsModel;
+}) => React.JSX.Element[];
+export default SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js

@@ -0,0 +1,30 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, color, strand = 1, coordStart = start, model, }) {
+    const { charactersPerRow, showCoordinates } = model;
+    return chunks.map((chunk, idx) => {
+        var _a;
+        const f = coordStart - (start % charactersPerRow);
+        const prefix = (idx == 0 && start % charactersPerRow == 0) || idx > 0
+            ? `${f + idx * strand * charactersPerRow}`.padStart(4) + '   '
+            : '';
+        const postfix = idx === chunks.length - 1 &&
+            (((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
+                (idx === 0 ? start % charactersPerRow : 0) !==
+                charactersPerRow
+            ? null
+            : showCoordinates
+                ? ' \n'
+                : '';
+        return (react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
+            showCoordinates ? prefix : null,
+            react_1.default.createElement("span", { style: { background: color } }, chunk),
+            postfix));
+    });
+});
+exports.default = SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts

@@ -4,3 +4,14 @@ export declare const proteinColor = "rgb(220,160,220)";
 export declare const cdsColor = "rgb(220,220,180)";
 export declare const updownstreamColor = "rgba(250,200,200)";
 export declare const genomeColor = "rgb(200,280,200)";
+export declare function splitString({ str, charactersPerRow, showCoordinates, currRemainder, splitSize, }: {
+    str: string;
+    charactersPerRow: number;
+    showCoordinates: boolean;
+    currRemainder?: number;
+    splitStart?: number;
+    splitSize?: number;
+}): {
+    segments: any[];
+    remainder: number;
+};

package/BaseFeatureWidget/SequenceFeatureDetails/util.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
+exports.splitString = splitString;
 // note that these are currently put into the style section instead of being
 // defined in classes to aid copy and paste to an external document e.g. word
 exports.intronColor = undefined;
@@ -9,3 +10,44 @@ exports.proteinColor = 'rgb(220,160,220)';
 exports.cdsColor = 'rgb(220,220,180)';
 exports.updownstreamColor = 'rgba(250,200,200)';
 exports.genomeColor = 'rgb(200,280,200)';
+function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0, splitSize = 10, }) {
+    var _a;
+    const numChunks = Math.ceil(str.length / charactersPerRow);
+    const chunks = new Array(numChunks);
+    let splitStart = currRemainder % 10;
+    let iter = 0;
+    let offset = 0;
+    for (; iter < numChunks + 1; ++iter) {
+        const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow;
+        const r = str.slice(offset, offset + inc);
+        if (!r) {
+            break;
+        }
+        if (showCoordinates) {
+            let res = '';
+            for (let i = 0, j = splitStart; i < r.length; i++, j++) {
+                // note: this adds a space at the start but it causes trouble to try to
+                // say e.g. j%splitSize==0 && j to try to only add non-zero spaces
+                if (j % splitSize === 0) {
+                    res += ' ';
+                    j = 0;
+                }
+                res += r[i];
+            }
+            if (res) {
+                chunks[iter] = res;
+            }
+        }
+        else {
+            chunks[iter] = r;
+        }
+        splitStart = 0; // after newline, reset
+        offset += inc;
+    }
+    return {
+        segments: chunks,
+        remainder: ((((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
+            (iter < 2 ? currRemainder : 0)) %
+            charactersPerRow,
+    };
+}

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -52,13 +52,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("../util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("../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]>;
@@ -132,13 +145,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("../util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("../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/BaseFeatureWidget/stateModelFactory.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = void 0;
+exports.stateModelFactory = stateModelFactory;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
 const clone_1 = __importDefault(require("clone"));
@@ -170,4 +170,3 @@ function stateModelFactory(pluginManager) {
         };
     });
 }
-exports.stateModelFactory = stateModelFactory;

package/BaseFeatureWidget/util.d.ts

@@ -25,16 +25,16 @@ export declare function dedupe(list: Feat[]): Feat[];
 export declare function revlist(list: Feat[], seqlen: number): {
     start: number;
     end: number;
-    type?: string | undefined;
-    name?: string | undefined;
-    id?: string | undefined;
+    type?: string;
+    name?: string;
+    id?: string;
 }[];
 export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
     type: string;
     start: number;
     end: number;
-    name?: string | undefined;
-    id?: string | undefined;
+    name?: string;
+    id?: string;
 }[];
 export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
     type: string;

package/BaseFeatureWidget/util.js

@@ -1,10 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ellipses = exports.calculateUTRs2 = exports.calculateUTRs = exports.revlist = exports.dedupe = exports.stitch = void 0;
+exports.stitch = stitch;
+exports.dedupe = dedupe;
+exports.revlist = revlist;
+exports.calculateUTRs = calculateUTRs;
+exports.calculateUTRs2 = calculateUTRs2;
+exports.ellipses = ellipses;
 function stitch(subfeats, sequence) {
     return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
 }
-exports.stitch = stitch;
 // filter items if they have the same "ID" or location
 function getItemId(feat) {
     return `${feat.start}-${feat.end}`;
@@ -13,7 +17,6 @@ function getItemId(feat) {
 function dedupe(list) {
     return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
 }
-exports.dedupe = dedupe;
 function revlist(list, seqlen) {
     return list
         .map(sub => ({
@@ -23,7 +26,6 @@ function revlist(list, seqlen) {
     }))
         .sort((a, b) => a.start - b.start);
 }
-exports.revlist = revlist;
 function calculateUTRs(cds, exons) {
     // checking length ensures the .at below are valid
     if (!cds.length) {
@@ -45,7 +47,6 @@ function calculateUTRs(cds, exons) {
     ].map(elt => ({ ...elt, type: 'three_prime_UTR' }));
     return [...fiveUTRs, ...threeUTRs];
 }
-exports.calculateUTRs = calculateUTRs;
 // calculates UTRs using impliedUTRs logic, but there are no exon subfeatures
 function calculateUTRs2(cds, parentFeat) {
     if (!cds.length) {
@@ -60,8 +61,6 @@ function calculateUTRs2(cds, parentFeat) {
     }));
     return [...fiveUTRs, ...threeUTRs];
 }
-exports.calculateUTRs2 = calculateUTRs2;
 function ellipses(slug) {
     return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
 }
-exports.ellipses = ellipses;

package/PluginLoader.js

@@ -3,7 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.pluginDescriptionString = exports.isCJSPluginDefinition = exports.isESMPluginDefinition = exports.isUMDPluginDefinition = void 0;
+exports.isUMDPluginDefinition = isUMDPluginDefinition;
+exports.isESMPluginDefinition = isESMPluginDefinition;
+exports.isCJSPluginDefinition = isCJSPluginDefinition;
+exports.pluginDescriptionString = pluginDescriptionString;
 const load_script_1 = __importDefault(require("load-script"));
 // locals
 const Plugin_1 = __importDefault(require("./Plugin"));
@@ -15,12 +18,10 @@ function isUMDPluginDefinition(def) {
         def.umdLoc !== undefined) &&
         def.name !== undefined);
 }
-exports.isUMDPluginDefinition = isUMDPluginDefinition;
 function isESMPluginDefinition(def) {
     return (def.esmUrl !== undefined ||
         def.esmLoc !== undefined);
 }
-exports.isESMPluginDefinition = isESMPluginDefinition;
 function promisifiedLoadScript(src) {
     return new Promise((resolve, reject) => {
         (0, load_script_1.default)(src, (err, script) => {
@@ -48,7 +49,6 @@ async function loadScript(scriptUrl) {
 function isCJSPluginDefinition(def) {
     return def.cjsUrl !== undefined;
 }
-exports.isCJSPluginDefinition = isCJSPluginDefinition;
 function pluginDescriptionString(pluginDefinition) {
     var _a;
     if (isUMDPluginDefinition(pluginDefinition)) {
@@ -63,7 +63,6 @@ function pluginDescriptionString(pluginDefinition) {
     }
     return 'unknown plugin';
 }
-exports.pluginDescriptionString = pluginDescriptionString;
 function isInWebWorker() {
     return Boolean('WorkerGlobalScope' in globalThis);
 }

package/PluginManager.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { IAnyType, IAnyModelType } from 'mobx-state-tree';
 import PluggableElementBase from './pluggableElementTypes/PluggableElementBase';
 import RendererType from './pluggableElementTypes/renderers/RendererType';
@@ -71,8 +70,8 @@ export default class PluginManager {
             [key: string]: (value: any, ...args: any[]) => any;
         }) => void;
         getFunction: (name: string) => (value: any, ...args: any[]) => any;
-        eval: (expression: string, context?: import("jexl/Expression").Context | undefined) => Promise<any>;
-        evalSync: (expression: string, context?: import("jexl/Expression").Context | undefined) => any;
+        eval: (expression: string, context?: import("jexl/Expression").Context) => Promise<any>;
+        evalSync: (expression: string, context?: import("jexl/Expression").Context) => any;
         compile: (expression: string) => import("jexl/Expression").default;
         createExpression: (expression: string) => import("jexl/Expression").default;
         removeOp: (operator: string) => void;
@@ -151,22 +150,13 @@ export default class PluginManager {
         '@jbrowse/core/util/tracks': typeof import("./util/tracks");
         '@jbrowse/core/util/Base1DViewModel': import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-                refName: import("mobx-state-tree").ISimpleType<string>;
-                start: import("mobx-state-tree").ISimpleType<number>;
-                end: import("mobx-state-tree").ISimpleType<number>;
-                reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-            } & {
-                assemblyName: import("mobx-state-tree").ISimpleType<string>;
-            }, {
-                setRefName(newRefName: string): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("./util").Region[], import("./util").Region[], import("./util").Region[]>, [undefined]>;
             bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
             offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
             interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
             minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         }, {
-            features: import("./util").Feature[] | undefined;
+            features: undefined | import("./util").Feature[];
             volatileWidth: number;
         } & {
             setDisplayedRegions(regions: import("./util").Region[]): void;
@@ -193,12 +183,12 @@ export default class PluginManager {
                 offset: number;
                 start: number;
                 end: number;
-                reversed: boolean;
+                reversed?: boolean;
             };
             bpToPx({ refName, coord, regionNumber, }: {
                 refName: string;
                 coord: number;
-                regionNumber?: number | undefined;
+                regionNumber?: number;
             }): number | undefined;
         } & {
             setFeatures(features: import("./util").Feature[]): void;
@@ -210,7 +200,7 @@ export default class PluginManager {
             centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
             scroll(distance: number): number;
         } & {
-            moveTo(start?: import("./util/Base1DUtils").BpOffset | undefined, end?: import("./util/Base1DUtils").BpOffset | undefined): void;
+            moveTo(start?: import("./util/Base1DUtils").BpOffset, end?: import("./util/Base1DUtils").BpOffset): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
         '@jbrowse/core/util/io': typeof import("./util/io");
         '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");

package/ReExports/modules.d.ts

@@ -59,22 +59,13 @@ declare const libs: {
     '@jbrowse/core/util/tracks': typeof trackUtils;
     '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
         id: mst.IOptionalIType<mst.ISimpleType<string>, [undefined]>;
-        displayedRegions: mst.IArrayType<mst.IModelType<{
-            refName: mst.ISimpleType<string>;
-            start: mst.ISimpleType<number>;
-            end: mst.ISimpleType<number>;
-            reversed: mst.IOptionalIType<mst.ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: mst.ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, mst._NotCustomized, mst._NotCustomized>>;
+        displayedRegions: mst.IOptionalIType<mst.IType<coreUtil.Region[], coreUtil.Region[], coreUtil.Region[]>, [undefined]>;
         bpPerPx: mst.IType<number | undefined, number, number>;
         offsetPx: mst.IType<number | undefined, number, number>;
         interRegionPaddingWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
         minimumBlockWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
     }, {
-        features: coreUtil.Feature[] | undefined;
+        features: undefined | coreUtil.Feature[];
         volatileWidth: number;
     } & {
         setDisplayedRegions(regions: coreUtil.Region[]): void;
@@ -101,12 +92,12 @@ declare const libs: {
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean;
         };
         bpToPx({ refName, coord, regionNumber, }: {
             refName: string;
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number;
         }): number | undefined;
     } & {
         setFeatures(features: coreUtil.Feature[]): void;
@@ -118,7 +109,7 @@ declare const libs: {
         centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
         scroll(distance: number): number;
     } & {
-        moveTo(start?: import("../util/Base1DUtils").BpOffset | undefined, end?: import("../util/Base1DUtils").BpOffset | undefined): void;
+        moveTo(start?: import("../util/Base1DUtils").BpOffset, end?: import("../util/Base1DUtils").BpOffset): void;
     }, mst._NotCustomized, mst._NotCustomized>;
     '@jbrowse/core/util/io': typeof coreIo;
     '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
@@ -146,12 +137,12 @@ declare const libs: {
         makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
             name?: string | Record<string, unknown> | undefined;
             uniqId?: string | undefined;
-        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
+        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material/styles").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
             props: Record<string, unknown>;
             ownerState?: Record<string, unknown> | undefined;
         } | undefined) => {
             classes: Record<RuleName, string>;
-            theme: MUIStyles.Theme;
+            theme: import("@mui/material/styles").Theme;
             css: import("tss-react").Css;
             cx: import("tss-react").Cx;
         };

package/TextSearch/TextSearchManager.d.ts

@@ -16,13 +16,17 @@ export default class TextSearchManager {
     relevantAdapters(searchScope: SearchScope): ({
         [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 & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     getAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): AnyConfigurationModel[];
     getTrackAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
         [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 & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     /**
      * Returns list of relevant results given a search query and options

package/assemblyManager/assembly.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 = assemblyFactory;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 // locals
@@ -375,7 +376,6 @@ function assemblyFactory(assemblyConfigType, pm) {
         },
     }));
 }
-exports.default = assemblyFactory;
 async function getRefNameAliases(config, pm, signal) {
     const type = pm.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();