@jbrowse/plugin-config 2.16.1 → 2.18.0

package/esm/ConfigurationEditorWidget/components/TypeSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const TypeSelector: ({ typeNameChoices, slot, slotName, onChange, }: {
     typeNameChoices: string[];
     slot: AnyConfigurationModel;

package/esm/ConfigurationEditorWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function registerConfigurationEditorWidget(pluginManager: PluginManager): void;

package/esm/ConfigurationEditorWidget/index.js

@@ -1,8 +1,8 @@
 import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './model';
 import HeadingComponent from './components/HeadingComponent';
+import stateModelFactory from './model';
 const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {});
 const LazyConfigurationEditorComponent = lazy(() => import('./components/ConfigurationEditor'));
 export default function registerConfigurationEditorWidget(pluginManager) {

package/esm/ConfigurationEditorWidget/model.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function stateModelFactory(pluginManager: PluginManager): 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">;

package/esm/ConfigurationEditorWidget/model.js

@@ -1,12 +1,10 @@
-import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
 export default function stateModelFactory(pluginManager) {
     return 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 => ({

package/esm/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -1,9 +1,9 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export declare function makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     protected features: Map<string, Feature[]>;

package/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -1,7 +1,7 @@
+import { readConfObject } from '@jbrowse/core/configuration';
 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';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 export function makeFeatures(fdata) {
     const features = new Map();
     for (const entry of fdata) {
@@ -14,7 +14,6 @@ export function makeFeatures(fdata) {
         }
         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'));
     }
@@ -47,5 +46,5 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/FromConfigAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/esm/FromConfigAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FromConfigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('FromConfigAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/esm/FromConfigAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigAdapterF(pluginManager: PluginManager): void;

package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts

@@ -1,18 +1,11 @@
-import { BaseAdapter, RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-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 }, ... ]`
- */
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class FromConfigRegionsAdapter extends BaseAdapter implements RegionsAdapter {
     private features;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    /**
-     * Get refName, start, and end for all features after collapsing any overlaps
-     */
     getRegions(): Promise<{
         refName: string;
         start: number;

package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -1,23 +1,14 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { makeFeatures } from '../FromConfigAdapter/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 f = readConfObject(config, 'features');
         this.features = makeFeatures(f);
     }
-    /**
-     * 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) {
@@ -41,9 +32,8 @@ export default class FromConfigRegionsAdapter extends BaseAdapter {
                 regions.push(currentRegion);
             }
         }
-        // sort the regions by refName
         regions.sort((a, b) => a.refName.localeCompare(b.refName));
         return regions;
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/FromConfigRegionsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const regionsConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/esm/FromConfigRegionsAdapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FromConfigRegionsAdapter
- * used for specifying refNames+sizes of an assembly
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/esm/FromConfigRegionsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigRegionsAdapterF(pluginManager: PluginManager): void;

package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts

@@ -1,26 +1,13 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
+import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class FromConfigSequenceAdapter extends FromConfigAdapter implements RegionsAdapter {
-    /**
-     * 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<{
         start: number;
         end: number;
         refName: string;
     }[]>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }

package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js

@@ -1,15 +1,9 @@
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
-// locals
 import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
-import { firstValueFrom } from 'rxjs';
 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) {
         return ObservableCreate(async (observer) => {
             const feats = await firstValueFrom(super.getFeatures(region).pipe(toArray()));
@@ -26,12 +20,8 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter {
             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) {
@@ -57,10 +47,5 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter {
         }
         return regions;
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/FromConfigSequenceAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const sequenceConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/esm/FromConfigSequenceAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FromConfigSequenceAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/esm/FromConfigSequenceAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigSequenceAdapterF(pluginManager: PluginManager): void;

package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts

@@ -1,4 +1,5 @@
-import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseRefNameAliasAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
     getRefNameAliases(): Promise<{
         refName: string;

package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js

@@ -1,4 +1,4 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 export default class NcbiSequenceReportAliasAdapter extends BaseAdapter {
     async getRefNameAliases() {

package/esm/NcbiSequenceReportAliasAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     location: {
         type: string;
         defaultValue: {

package/esm/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config NcbiSequenceReportAliasAdapter
- * can read "sequence_report.tsv" type files from NCBI
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequenceReportAliasAdapter', {
-    /**
-     * #slot
-     */
     location: {
         type: 'fileLocation',
         defaultValue: {

package/esm/NcbiSequenceReportAliasAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function NcbiSequenceReportAliasAdapterF(pluginManager: PluginManager): void;

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.d.ts

@@ -1,4 +1,5 @@
-import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseRefNameAliasAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
     getRefNameAliases(): Promise<{
         refName: string;

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -1,4 +1,4 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 export default class RefNameAliasAdapter extends BaseAdapter {
     async getRefNameAliases() {

package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     location: {
         type: string;
         defaultValue: {
@@ -9,11 +6,6 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-    /**
-     * #slot
-     * by default, the "ref names that match the fasta" are assumed to be in the
-     * first column (0), change this variable if needed
-     */
     refNameColumn: {
         type: string;
         defaultValue: number;

package/esm/RefNameAliasAdapter/configSchema.js

@@ -1,14 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config RefNameAliasAdapter
- * can read "chromAliases" type files from UCSC or any tab separated file of
- * refName aliases
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
-    /**
-     * #slot
-     */
     location: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,11 +8,6 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     * by default, the "ref names that match the fasta" are assumed to be in the
-     * first column (0), change this variable if needed
-     */
     refNameColumn: {
         type: 'number',
         defaultValue: 0,

package/esm/RefNameAliasAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function RefNameAliasAdapterF(pluginManager: PluginManager): void;

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model, }: {
     model: {
         target: import("@jbrowse/core/configuration").AnyConfigurationModel;

package/esm/index.js

@@ -1,11 +1,11 @@
 import { lazy } from 'react';
 import Plugin from '@jbrowse/core/Plugin';
+import ConfigurationEditorWidgetF from './ConfigurationEditorWidget';
 import FromConfigAdapterF from './FromConfigAdapter';
 import FromConfigRegionsAdapterF from './FromConfigRegionsAdapter';
 import FromConfigSequenceAdapterF from './FromConfigSequenceAdapter';
-import RefNameAliasAdapterF from './RefNameAliasAdapter';
-import ConfigurationEditorWidgetF from './ConfigurationEditorWidget';
 import NcbiSequenceReportAliasAdapterF from './NcbiSequenceReportAliasAdapter';
+import RefNameAliasAdapterF from './RefNameAliasAdapter';
 const LazyConfigurationEditorComponent = lazy(() => import('./ConfigurationEditorWidget/components/ConfigurationEditor'));
 export default class ConfigurationPlugin extends Plugin {
     constructor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }