@jbrowse/plugin-sequence 1.7.11 → 2.1.0

package/esm/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -0,0 +1,26 @@
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class TwoBitAdapter extends BaseSequenceAdapter {
+    private twobit;
+    protected chromSizesData: Promise<Record<string, number> | undefined>;
+    private initChromSizes;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(): Promise<string[]>;
+    getRegions(): Promise<NoAssemblyRegion[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -0,0 +1,79 @@
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { TwoBitFile } from '@gmod/twobit';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class TwoBitAdapter extends BaseSequenceAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.chromSizesData = this.initChromSizes();
+        this.twobit = new TwoBitFile({
+            filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
+        });
+    }
+    async initChromSizes() {
+        const conf = readConfObject(this.config, 'chromSizesLocation');
+        // check against default and empty in case someone makes the field blank in
+        // config editor, may want better way to check "optional config slots" in
+        // future
+        if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
+            const file = openLocation(conf, this.pluginManager);
+            const data = await file.readFile('utf8');
+            return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(line => !!line.trim()).map(line => {
+                const [name, length] = line.split('\t');
+                return [name, +length];
+            }));
+        }
+        return undefined;
+    }
+    async getRefNames() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData);
+        }
+        return this.twobit.getSequenceNames();
+    }
+    async getRegions() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData).map(refName => ({
+                refName,
+                start: 0,
+                end: chromSizesData[refName],
+            }));
+        }
+        const refSizes = await this.twobit.getSequenceSizes();
+        return Object.keys(refSizes).map(refName => ({
+            refName,
+            start: 0,
+            end: refSizes[refName],
+        }));
+    }
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures({ refName, start, end }) {
+        return ObservableCreate(async (observer) => {
+            const size = await this.twobit.getSequenceSize(refName);
+            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const seq = await this.twobit.getSequence(refName, start, regionEnd);
+            if (seq) {
+                observer.next(new SimpleFeature({
+                    id: `${refName} ${start}-${regionEnd}`,
+                    data: { refName, start, end: regionEnd, seq },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=TwoBitAdapter.js.map

package/esm/TwoBitAdapter/TwoBitAdapter.js.map

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package/esm/TwoBitAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/TwoBitAdapter/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('TwoBitAdapter', {
+    twoBitLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
+    },
+    chromSizesLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/default.chrom.sizes',
+            locationType: 'UriLocation',
+        },
+        description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/TwoBitAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/TwoBitAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/TwoBitAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/TwoBitAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class SequencePlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,197 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import Plugin from '@jbrowse/core/Plugin';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import { makeIndex, getFileName, } from '@jbrowse/core/util/tracks';
+import { configSchema as bgzipFastaAdapterConfigSchema } from './BgzipFastaAdapter';
+import { configSchema as chromSizesAdapterConfigSchema } from './ChromSizesAdapter';
+import { configSchema as divSequenceRendererConfigSchema, ReactComponent as DivSequenceRendererReactComponent, } from './DivSequenceRenderer';
+import { configSchema as indexedFastaAdapterConfigSchema } from './IndexedFastaAdapter';
+import { configSchema as linearReferenceSequenceDisplayConfigSchema, modelFactory as linearReferenceSequenceDisplayModelFactory, } from './LinearReferenceSequenceDisplay';
+import { configSchema as twoBitAdapterConfigSchema } from './TwoBitAdapter';
+import GCContentAdapterF from './GCContentAdapter';
+import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig';
+/* adjust in both directions */
+class DivSequenceRenderer extends FeatureRendererType {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    getExpandedRegion(region) {
+        return {
+            ...region,
+            start: Math.max(region.start - 3, 0),
+            end: region.end + 3,
+        };
+    }
+}
+export default class SequencePlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'SequencePlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'TwoBitAdapter',
+            configSchema: twoBitAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./TwoBitAdapter/TwoBitAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.2bit$/i;
+                const adapterName = 'TwoBitAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    twoBitLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'TwoBitAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'ChromSizesAdapter',
+            configSchema: chromSizesAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./ChromSizesAdapter/ChromSizesAdapter').then(r => r.default),
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'IndexedFastaAdapter',
+            configSchema: indexedFastaAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./IndexedFastaAdapter/IndexedFastaAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+                const adapterName = 'IndexedFastaAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    fastaLocation: file,
+                    faiLocation: index || makeIndex(file, '.fai'),
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'IndexedFastaAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'BgzipFastaAdapter',
+            configSchema: bgzipFastaAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./BgzipFastaAdapter/BgzipFastaAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+                const adapterName = 'BgzipFastaAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    faiLocation: makeIndex(file, '.fai'),
+                    gziLocation: makeIndex(file, '.gzi'),
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'BgzipFastaAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'GCContentAdapter',
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            ...pluginManager.load(GCContentAdapterF),
+        }));
+        pluginManager.addTrackType(() => {
+            const configSchema = createReferenceSeqTrackConfig(pluginManager);
+            return new TrackType({
+                name: 'ReferenceSequenceTrack',
+                configSchema,
+                stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
+            });
+        });
+        pluginManager.addDisplayType(() => {
+            const stateModel = linearReferenceSequenceDisplayModelFactory(linearReferenceSequenceDisplayConfigSchema);
+            return {
+                name: 'LinearReferenceSequenceDisplay',
+                configSchema: linearReferenceSequenceDisplayConfigSchema,
+                stateModel,
+                trackType: 'ReferenceSequenceTrack',
+                viewType: 'LinearGenomeView',
+                ReactComponent: BaseLinearDisplayComponent,
+            };
+        });
+        pluginManager.addRendererType(() => new DivSequenceRenderer({
+            name: 'DivSequenceRenderer',
+            ReactComponent: DivSequenceRendererReactComponent,
+            configSchema: divSequenceRendererConfigSchema,
+            pluginManager,
+        }));
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/esm/referenceSeqTrackConfig.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/referenceSeqTrackConfig.js

@@ -0,0 +1,63 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { types } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/*
+Note: this is primarily a copy of createBaseTrackConfig, except with a subset
+of the config slots, to avoid including fields that don't make sense for the
+ReferenceSequenceTrack
+*/
+export function createReferenceSeqTrackConfig(pluginManager) {
+    return ConfigurationSchema('ReferenceSequenceTrack', {
+        adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+        name: {
+            type: 'string',
+            description: 'optional track name',
+            defaultValue: '',
+        },
+        metadata: {
+            type: 'frozen',
+            description: 'anything to add about this track',
+            defaultValue: {},
+        },
+    }, {
+        preProcessSnapshot: s => {
+            const snap = JSON.parse(JSON.stringify(s));
+            const displayTypes = new Set();
+            const { displays = [] } = snap;
+            if (snap.trackId !== 'placeholderId') {
+                // Gets the displays on the track snapshot and the possible displays
+                // from the track type and adds any missing possible displays to the
+                // snapshot
+                displays.forEach((d) => d && displayTypes.add(d.type));
+                const trackType = pluginManager.getTrackType(snap.type);
+                trackType.displayTypes.forEach(displayType => {
+                    if (!displayTypes.has(displayType.name)) {
+                        displays.push({
+                            displayId: `${snap.trackId}-${displayType.name}`,
+                            type: displayType.name,
+                        });
+                    }
+                });
+            }
+            return { ...snap, displays };
+        },
+        explicitIdentifier: 'trackId',
+        explicitlyTyped: true,
+        actions: (self) => ({
+            addDisplayConf(displayConf) {
+                const { type } = displayConf;
+                if (!type) {
+                    throw new Error(`unknown display type ${type}`);
+                }
+                const display = self.displays.find((d) => d && d.displayId === displayConf.displayId);
+                if (display) {
+                    return display;
+                }
+                const length = self.displays.push(displayConf);
+                return self.displays[length - 1];
+            },
+        }),
+    });
+}
+//# sourceMappingURL=referenceSeqTrackConfig.js.map

package/esm/referenceSeqTrackConfig.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.7.11",
+  "version": "2.1.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,32 +20,36 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/sequence",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@gmod/indexedfasta": "^2.0.2",
     "@gmod/twobit": "^1.1.12",
-    "abortable-promise-cache": "^1.5.0",
-    "generic-filehandle": "^2.2.2"
+    "abortable-promise-cache": "^1.5.0"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@jbrowse/plugin-wiggle": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@jbrowse/plugin-wiggle": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0"
@@ -53,5 +57,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
 }

package/src/ChromSizesAdapter/ChromSizesAdapter.ts

@@ -2,56 +2,40 @@ import {
   RegionsAdapter,
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { GenericFilehandle } from 'generic-filehandle'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { Instance } from 'mobx-state-tree'
-import MyConfigSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends BaseAdapter implements RegionsAdapter {
   // the map of refSeq to length
-  protected refSeqs: Promise<Record<string, number>>
+  protected setupP?: Promise<{ [key: string]: number }>
 
-  protected source: string
-
-  public constructor(
-    config: Instance<typeof MyConfigSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const chromSizesLocation = readConfObject(config, 'chromSizesLocation')
-    if (!chromSizesLocation) {
-      throw new Error('must provide chromSizesLocation')
-    }
-    const file = openLocation(
-      chromSizesLocation as FileLocation,
-      this.pluginManager,
+  async setupPre() {
+    const pm = this.pluginManager
+    const file = openLocation(this.getConf('chromSizesLocation'), pm)
+    const data = await file.readFile('utf8')
+    return Object.fromEntries(
+      data
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f)
+        .map((line: string) => {
+          const [name, length] = line.split('\t')
+          return [name, +length]
+        }),
     )
-    this.source = file.toString()
-    this.refSeqs = this.init(file)
   }
 
-  private async init(file: GenericFilehandle) {
-    const data = await file.readFile('utf8')
-    const refSeqs: { [key: string]: number } = {}
-    if (!data.length) {
-      throw new Error(`Could not read file ${file.toString()}`)
+  async setup() {
+    if (!this.setupP) {
+      this.setupP = this.setupPre().catch(e => {
+        this.setupP = undefined
+        throw e
+      })
     }
-    data.split('\n').forEach((line: string) => {
-      if (line.length) {
-        const [name, length] = line.split('\t')
-        refSeqs[name] = +length
-      }
-    })
-    return refSeqs
+    return this.setupP
   }
 
   public async getRegions() {
-    const refSeqs = await this.refSeqs
+    const refSeqs = await this.setup()
     return Object.keys(refSeqs).map(refName => ({
       refName,
       start: 0,
@@ -59,10 +43,6 @@ export default class extends BaseAdapter implements RegionsAdapter {
     }))
   }
 
-  public getFeatures() {
-    throw new Error('sequence not available')
-  }
-
   public getHeader() {
     return {}
   }

package/src/DivSequenceRenderer/components/DivSequenceRendering.test.js

@@ -4,7 +4,7 @@ import { render } from '@testing-library/react'
 import { createJBrowseTheme } from '@jbrowse/core/ui'
 import PrecomputedLayout from '@jbrowse/core/util/layouts/PrecomputedLayout'
 import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import { ThemeProvider } from '@material-ui/core'
+import { ThemeProvider } from '@mui/material'
 import DivSequenceRendering from './DivSequenceRendering'
 import DivRenderingConfigSchema from '../configSchema'
 

package/src/LinearReferenceSequenceDisplay/model.ts

@@ -3,8 +3,10 @@ import {
   BaseLinearDisplay,
   LinearGenomeViewModel,
 } from '@jbrowse/plugin-linear-genome-view'
-import { ConfigurationReference } from '@jbrowse/core/configuration'
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  AnyConfigurationSchemaType,
+  ConfigurationReference,
+} from '@jbrowse/core/configuration'
 import { getContainingView } from '@jbrowse/core/util'
 
 export function modelFactory(configSchema: AnyConfigurationSchemaType) {