@jbrowse/plugin-config 2.17.0 → 2.18.0

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": "2.17.0",
+  "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": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }