@jbrowse/core 1.6.5 → 1.6.8

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -29,8 +29,6 @@ var _core = require("@material-ui/core");
 
 var _ExpandMore = _interopRequireDefault(require("@material-ui/icons/ExpandMore"));
 
-var _styles = require("@material-ui/core/styles");
-
 var _xDataGrid = require("@mui/x-data-grid");
 
 var _mobxReact = require("mobx-react");
@@ -64,7 +62,7 @@ var MAX_FIELD_NAME_WIDTH = 170; // these are always omitted as too detailed
 var globalOmit = ['length', 'position', 'subfeatures', 'uniqueId', 'exonFrames', 'parentId', 'thickStart', 'thickEnd']; // coreDetails are omitted in some circumstances
 
 var coreDetails = ['name', 'start', 'end', 'strand', 'refName', 'description', 'type'];
-var useStyles = (0, _styles.makeStyles)(function (theme) {
+var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
     expansionPanelDetails: {
       display: 'block',

package/BaseFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '../PluginManager';
-declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const configSchema: import("../configuration").AnyConfigurationSchemaType;
 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<"BaseFeatureWidget">;

package/PluginLoader.d.ts

@@ -1,5 +1,5 @@
 import { PluginConstructor } from './Plugin';
-export declare const PluginSourceConfigurationSchema: import("./configuration/configurationSchema").AnyConfigurationSchemaType;
+export declare const PluginSourceConfigurationSchema: import("./configuration").AnyConfigurationSchemaType;
 export interface UMDPluginDefinition {
     umdUrl: string;
     name: string;

package/PluginManager.d.ts

@@ -205,6 +205,7 @@ export default class PluginManager {
         '@jbrowse/core/util/layouts': typeof import("./util/layouts");
         '@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>;
@@ -220,7 +221,7 @@ export default class PluginManager {
             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/simpleFeature").Feature[] | undefined;
+            features: import("./util").Feature[] | undefined;
             volatileWidth: number;
         } & {
             setDisplayedRegions(regions: import("./util").Region[]): void;
@@ -228,6 +229,7 @@ export default class PluginManager {
             setVolatileWidth(width: number): void;
         } & {
             readonly width: number;
+            readonly assemblyNames: string[];
             readonly displayedRegionsTotalPx: number;
             readonly maxOffset: number;
             readonly minOffset: number;
@@ -262,7 +264,7 @@ export default class PluginManager {
                 regionNumber?: number | undefined;
             }): number | undefined;
         } & {
-            setFeatures(features: import("./util/simpleFeature").Feature[]): void;
+            setFeatures(features: import("./util").Feature[]): void;
             zoomToDisplayedRegions(leftPx: import("./util/Base1DViewModel").BpOffset | undefined, rightPx: import("./util/Base1DViewModel").BpOffset | undefined): void;
             showAllRegions(): void;
             moveTo(start: import("./util/Base1DViewModel").BpOffset, end: import("./util/Base1DViewModel").BpOffset): void;

package/ReExports/modules.d.ts

@@ -133,6 +133,7 @@ declare const libs: {
     '@jbrowse/core/util/layouts': typeof coreLayouts;
     '@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>;
@@ -148,7 +149,7 @@ declare const libs: {
         interRegionPaddingWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
         minimumBlockWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
     }, {
-        features: import("../util/simpleFeature").Feature[] | undefined;
+        features: coreUtil.Feature[] | undefined;
         volatileWidth: number;
     } & {
         setDisplayedRegions(regions: coreUtil.Region[]): void;
@@ -156,6 +157,7 @@ declare const libs: {
         setVolatileWidth(width: number): void;
     } & {
         readonly width: number;
+        readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
         readonly maxOffset: number;
         readonly minOffset: number;
@@ -190,7 +192,7 @@ declare const libs: {
             regionNumber?: number | undefined;
         }): number | undefined;
     } & {
-        setFeatures(features: import("../util/simpleFeature").Feature[]): void;
+        setFeatures(features: coreUtil.Feature[]): void;
         zoomToDisplayedRegions(leftPx: import("../util/Base1DViewModel").BpOffset | undefined, rightPx: import("../util/Base1DViewModel").BpOffset | undefined): void;
         showAllRegions(): void;
         moveTo(start: import("../util/Base1DViewModel").BpOffset, end: import("../util/Base1DViewModel").BpOffset): void;

package/TextSearch/TextSearchManager.d.ts

@@ -29,10 +29,10 @@ export default class TextSearchManager {
      */
     relevantAdapters(searchScope: SearchScope): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType>)[];
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     getAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType>)[];
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     /**
      * Returns list of relevant results given a search query and options
      * @param args - search options/arguments include: search query

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '../PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const _default: (pluginManager: PluginManager) => import("../configuration").AnyConfigurationSchemaType;
 export default _default;

package/assemblyManager/assemblyManager.d.ts

@@ -9,7 +9,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -31,14 +31,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -65,7 +65,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -87,14 +87,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -119,7 +119,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -141,14 +141,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -169,7 +169,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     readonly assemblyNamesList: string[];
     readonly assemblyList: (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType> & {
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType> & {
         name: string;
     })[];
     readonly rpcManager: any;
@@ -184,7 +184,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -206,14 +206,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -238,7 +238,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -260,14 +260,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -307,7 +307,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -329,14 +329,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -361,7 +361,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -383,14 +383,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{

package/configuration/index.d.ts

@@ -1,3 +1,3 @@
 export { ConfigurationSchema, ConfigurationReference, } from './configurationSchema';
-export type { AnyConfigurationModel } from './configurationSchema';
+export type { AnyConfigurationModel, AnyConfigurationSchemaType, } from './configurationSchema';
 export * from './util';

package/configuration/util.js

@@ -89,11 +89,7 @@ function readConfObject(confObject) {
       subConf = confObject.get(slotName);
     }
 
-    if (!subConf) {
-      return undefined;
-    }
-
-    return readConfObject(subConf, newPath, args);
+    return subConf ? readConfObject(subConf, newPath, args) : undefined;
   }
 
   return readConfObject(confObject, slotName, args);

package/data_adapters/BaseAdapter.d.ts

@@ -1,6 +1,6 @@
 import { Observable } from 'rxjs';
 import { Feature } from '../util/simpleFeature';
-import { AnyConfigurationModel } from '../configuration/configurationSchema';
+import { AnyConfigurationModel } from '../configuration';
 import { getSubAdapterType } from './dataAdapterCache';
 import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
 import BaseResult from '../TextSearch/BaseResults';
@@ -59,6 +59,7 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * @param opts - Feature adapter options
      */
     abstract getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getConf(arg: string | string[]): any;
     /**
      * Get features from the data source that overlap a region
      * @param region - Region