@jbrowse/plugin-config 1.7.9 → 2.0.0

package/esm/ConfigurationEditorWidget/components/SlotEditor.js.map

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/components/StringArrayEditor.d.ts

@@ -0,0 +1,12 @@
+/// <reference types="react" />
+declare const StringArrayEditor: ({ slot, }: {
+    slot: {
+        name: string;
+        value: string[];
+        setAtIndex: Function;
+        removeAtIndex: Function;
+        add: Function;
+        description: string;
+    };
+}) => JSX.Element;
+export default StringArrayEditor;

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -0,0 +1,36 @@
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, FormHelperText, IconButton, InputAdornment, InputLabel, List, ListItem, TextField, } from '@mui/material';
+// icons
+import DeleteIcon from '@mui/icons-material/Delete';
+const StringArrayEditor = observer(({ slot, }) => {
+    const [value, setValue] = useState('');
+    const [addNew, setAddNew] = useState(false);
+    return (React.createElement(React.Fragment, null,
+        slot.name ? React.createElement(InputLabel, null, slot.name) : null,
+        React.createElement(List, { disablePadding: true },
+            slot.value.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
+                React.createElement(TextField, { value: val, onChange: evt => slot.setAtIndex(idx, evt.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(IconButton, { color: "secondary", onClick: () => slot.removeAtIndex(idx) },
+                                React.createElement(DeleteIcon, null)))),
+                    } })))),
+            addNew ? (React.createElement(ListItem, { disableGutters: true },
+                React.createElement(TextField, { value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(React.Fragment, null,
+                                React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 2 }, "data-testid": `stringArrayAdd-${slot.name}`, onClick: () => {
+                                        setAddNew(false);
+                                        slot.add(value);
+                                        setValue('');
+                                    } }, "OK"),
+                                React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 2 }, onClick: () => {
+                                        setAddNew(false);
+                                        setValue('');
+                                    } }, "Cancel")))),
+                    } }))) : null,
+            React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => setAddNew(true) }, "Add item")),
+        React.createElement(FormHelperText, null, slot.description)));
+});
+export default StringArrayEditor;
+//# sourceMappingURL=StringArrayEditor.js.map

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js.map

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/components/TypeSelector.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const TypeSelector: ({ typeNameChoices, slot, slotName, onChange, }: {
+    typeNameChoices: string[];
+    slot: AnyConfigurationModel;
+    slotName: string;
+    onChange: (event: React.ChangeEvent<HTMLInputElement>) => void;
+}) => JSX.Element;
+export default TypeSelector;

package/esm/ConfigurationEditorWidget/components/TypeSelector.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import { MenuItem, Paper, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { useSlotEditorStyles } from './SlotEditor';
+const TypeSelector = observer(({ typeNameChoices, slot, slotName, onChange, }) => {
+    const { classes } = useSlotEditorStyles();
+    return (React.createElement(Paper, { className: classes.paper },
+        React.createElement("div", { className: classes.paperContent },
+            React.createElement(TextField, { value: slot.type, label: "Type", select: true, helperText: `Type of ${slotName} to use`, fullWidth: true, onChange: onChange }, typeNameChoices.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))))));
+});
+export default TypeSelector;
+//# sourceMappingURL=TypeSelector.js.map

package/esm/ConfigurationEditorWidget/components/TypeSelector.js.map

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

@@ -0,0 +1,3 @@
+export { default as stateModelFactory } from "./model";
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export const HeadingComponent: import("mobx-react/dist/types/IReactComponent").IReactComponent<any>;

package/esm/ConfigurationEditorWidget/index.js

@@ -0,0 +1,20 @@
+import { observer } from 'mobx-react';
+import { isStateTreeNode, getType } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export { default as stateModelFactory } from './model';
+export const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {});
+export const HeadingComponent = observer(({ model }) => {
+    if (model === null || model === void 0 ? void 0 : model.target) {
+        if (model.target.type) {
+            return `${model.target.type} settings`;
+        }
+        if (isStateTreeNode(model.target)) {
+            const type = getType(model.target);
+            if (type === null || type === void 0 ? void 0 : type.name) {
+                return `${type.name.replace('ConfigurationSchema', '')} settings`;
+            }
+        }
+    }
+    return 'Settings';
+});
+//# sourceMappingURL=index.js.map

package/esm/ConfigurationEditorWidget/index.js.map

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

@@ -0,0 +1,8 @@
+declare function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"ConfigurationEditorWidget">;
+    target: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<any>>;
+}, {
+    setTarget(newTarget: any): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default _default;

package/esm/ConfigurationEditorWidget/model.js

@@ -0,0 +1,16 @@
+import { types } from 'mobx-state-tree';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+export default pluginManager => types
+    .model('ConfigurationEditorWidget', {
+    id: ElementId,
+    type: types.literal('ConfigurationEditorWidget'),
+    // If you add different types of targets, don't forget to account for that
+    // in the key of ./components/ConfigurationEditor.js
+    target: types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
+})
+    .actions(self => ({
+    setTarget(newTarget) {
+        self.target = newTarget;
+    },
+}));
+//# sourceMappingURL=model.js.map

package/esm/ConfigurationEditorWidget/model.js.map

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

@@ -0,0 +1,24 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature, { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigAdapter extends BaseFeatureDataAdapter {
+    protected features: Map<string, Feature[]>;
+    constructor(conf: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    static makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
+    static makeFeature(data: SimpleFeatureSerialized): SimpleFeature;
+    getRefNames(): Promise<string[]>;
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: any;
+    }[]>;
+    getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -0,0 +1,63 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { readConfObject } from '@jbrowse/core/configuration';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigAdapter extends BaseFeatureDataAdapter {
+    constructor(conf, getSubAdapter, pluginManager) {
+        super(conf, getSubAdapter, pluginManager);
+        const feats = readConfObject(conf, 'features');
+        this.features = FromConfigAdapter.makeFeatures(feats || []);
+    }
+    static makeFeatures(fdata) {
+        const features = new Map();
+        for (let i = 0; i < fdata.length; i += 1) {
+            if (fdata[i]) {
+                const f = this.makeFeature(fdata[i]);
+                const refName = f.get('refName');
+                let bucket = features.get(refName);
+                if (!bucket) {
+                    bucket = [];
+                    features.set(refName, bucket);
+                }
+                bucket.push(f);
+            }
+        }
+        // sort the features on each reference sequence by start coordinate
+        for (const refFeatures of features.values()) {
+            refFeatures.sort((a, b) => a.get('start') - b.get('start'));
+        }
+        return features;
+    }
+    static makeFeature(data) {
+        return new SimpleFeature(data);
+    }
+    async getRefNames() {
+        return [...this.features.keys()];
+    }
+    async getRefNameAliases() {
+        return Array.from(this.features.values()).map(featureArray => ({
+            refName: featureArray[0].get('refName'),
+            aliases: featureArray[0].get('aliases'),
+        }));
+    }
+    getFeatures(region) {
+        const { refName, start, end } = region;
+        return ObservableCreate(async (observer) => {
+            const features = this.features.get(refName) || [];
+            for (let i = 0; i < features.length; i++) {
+                const f = features[i];
+                if (f.get('end') > start && f.get('start') < end) {
+                    observer.next(f);
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigAdapter.js.map

package/esm/FromConfigAdapter/FromConfigAdapter.js.map

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package/esm/FromConfigAdapter/FromConfigRegionsAdapter.d.ts

@@ -0,0 +1,23 @@
+import { BaseAdapter, RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { configSchema as FromConfigAdapterConfigSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigRegionsAdapter extends BaseAdapter implements RegionsAdapter {
+    private features;
+    constructor(config: ConfigurationModel<typeof FromConfigAdapterConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -0,0 +1,50 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { readConfObject } from '@jbrowse/core/configuration';
+import FromConfigAdapter from './FromConfigAdapter';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigRegionsAdapter extends BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const features = readConfObject(config, 'features');
+        this.features = FromConfigAdapter.makeFeatures(features || []);
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    async getRegions() {
+        const regions = [];
+        // recall: features are stored in this object sorted by start coordinate
+        for (const [refName, features] of this.features) {
+            let currentRegion;
+            for (const feature of features) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
+                }
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
+                    }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
+                }
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        // sort the regions by refName
+        regions.sort((a, b) => a.refName.localeCompare(b.refName));
+        return regions;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigRegionsAdapter.js.map

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js.map

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

@@ -0,0 +1,25 @@
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import FromConfigAdapter from './FromConfigAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+    /**
+     * Fetch features for a certain region
+     * @param region - Region
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    /**
+     * 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/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -0,0 +1,73 @@
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { toArray } from 'rxjs/operators';
+import FromConfigAdapter from './FromConfigAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+    /**
+     * Fetch features for a certain region
+     * @param region - Region
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region) {
+        // TODO: restore commented version below once TSDX supports Rollup v2
+        // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
+        // return ObservableCreate<Feature>(async observer => {
+        //   const feats = await super.getFeatures(region).pipe(toArray()).toPromise()
+        const superGetFeatures = super.getFeatures;
+        return ObservableCreate(async (observer) => {
+            const feats = await superGetFeatures
+                .call(this, region)
+                .pipe(toArray())
+                .toPromise();
+            const feat = feats[0];
+            observer.next(new SimpleFeature({
+                ...feat.toJSON(),
+                uniqueId: `${feat.id()}:${region.start}-${region.end}`,
+                end: region.end,
+                start: region.start,
+                seq: feat
+                    .get('seq')
+                    .slice(Math.max(region.start - feat.get('start'), 0), Math.max(region.end - feat.get('start'), 0)),
+            }));
+            observer.complete();
+        });
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    async getRegions() {
+        const regions = [];
+        // recall: features are stored in this object sorted by start coordinate
+        for (const [refName, features] of this.features) {
+            let currentRegion;
+            for (const feature of features) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
+                }
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
+                    }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
+                }
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        return regions;
+    }
+    /**
+     * 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=FromConfigSequenceAdapter.js.map

package/esm/FromConfigAdapter/FromConfigSequenceAdapter.js.map

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

@@ -0,0 +1,3 @@
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const regionsConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const sequenceConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/FromConfigAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export const configSchema = ConfigurationSchema('FromConfigAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+export const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+export const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
+    features: {
+        type: 'frozen',
+        defaultValue: [],
+    },
+    featureClass: {
+        type: 'string',
+        defaultValue: 'SimpleFeature',
+    },
+}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+//# sourceMappingURL=configSchema.js.map

package/esm/FromConfigAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,mBAAmB,EACnB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,MAAM,CAAC,MAAM,mBAAmB,GAAG,mBAAmB,CACpD,0BAA0B,EAC1B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,MAAM,CAAC,MAAM,oBAAoB,GAAG,mBAAmB,CACrD,2BAA2B,EAC3B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}

package/esm/FromConfigAdapter/index.d.ts

@@ -0,0 +1,4 @@
+export { default as AdapterClass } from './FromConfigAdapter';
+export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
+export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
+export { configSchema, regionsConfigSchema, sequenceConfigSchema, } from './configSchema';

package/esm/FromConfigAdapter/index.js

@@ -0,0 +1,5 @@
+export { default as AdapterClass } from './FromConfigAdapter';
+export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
+export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
+export { configSchema, regionsConfigSchema, sequenceConfigSchema, } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/FromConfigAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,4BAA4B,CAAA;AAC3E,OAAO,EAAE,OAAO,IAAI,oBAAoB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,oBAAoB,GACrB,MAAM,gBAAgB,CAAA"}

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.d.ts

@@ -0,0 +1,8 @@
+import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: string[];
+    }[]>;
+    freeResources(): Promise<void>;
+}

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -0,0 +1,24 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class RefNameAliasAdapter extends BaseAdapter {
+    async getRefNameAliases() {
+        const loc = readConfObject(this.config, 'location');
+        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
+            return [];
+        }
+        const results = await openLocation(loc).readFile('utf8');
+        const refColumn = readConfObject(this.config, 'refNameColumn');
+        return results
+            .trim()
+            .split('\n')
+            .filter(f => !!f && !f.startsWith('#'))
+            .map(row => {
+            const aliases = row.split('\t');
+            const [refName] = aliases.splice(refColumn, 1);
+            return { refName, aliases: aliases.filter(f => !!f.trim()) };
+        });
+    }
+    async freeResources() { }
+}
+//# sourceMappingURL=RefNameAliasAdapter.js.map

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js.map

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

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

package/esm/RefNameAliasAdapter/configSchema.js

@@ -0,0 +1,15 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('RefNameAliasAdapter', {
+    location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/aliases.txt',
+            locationType: 'UriLocation',
+        },
+    },
+    refNameColumn: {
+        type: 'number',
+        defaultValue: 0,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/RefNameAliasAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,qBAAqB,EACrB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/RefNameAliasAdapter/index.d.ts

@@ -0,0 +1,2 @@
+export { default as AdapterClass } from './RefNameAliasAdapter';
+export { default as configSchema } from './configSchema';

package/esm/RefNameAliasAdapter/index.js

@@ -0,0 +1,3 @@
+export { default as AdapterClass } from './RefNameAliasAdapter';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/RefNameAliasAdapter/index.js.map

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

package/esm/index.d.ts

@@ -0,0 +1,18 @@
+/// <reference types="react" />
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model }: {
+    model: {
+        target: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    };
+}) => JSX.Element>;
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}
+export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor';
+export { LazyConfigurationEditorComponent as ConfigurationEditor };