@jbrowse/product-core 3.7.0 → 4.0.1

package/esm/RootModel/BaseRootModel.d.ts

@@ -2,19 +2,19 @@ import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
-import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
+import type { IAnyType, Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
 export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
     pluginManager: PluginManager;
     jbrowseModelType: IAnyType;
     sessionModelType: IAnyType;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
-}): import("mobx-state-tree").IModelType<{
+}): import("@jbrowse/mobx-state-tree").IModelType<{
     jbrowse: IAnyType;
-    session: import("mobx-state-tree").IMaybe<IAnyType>;
-    sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+    session: import("@jbrowse/mobx-state-tree").IMaybe<IAnyType>;
+    sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -22,6 +22,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -45,9 +46,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -62,6 +64,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -80,17 +83,18 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }, {
         readonly assemblyNameMap: Record<string, {
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -114,9 +118,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -131,6 +136,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -149,8 +155,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -158,6 +164,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -181,9 +188,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -198,6 +206,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -216,19 +225,20 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
     } & {
         getCanonicalAssemblyName(asmName: string): string | undefined;
         getCanonicalAssemblyName2(asmName: string): string;
         get(asmName: string): ({
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -252,9 +262,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -269,6 +280,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -287,8 +299,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -296,6 +308,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -319,9 +332,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -336,6 +350,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -354,20 +369,21 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
         readonly assemblyNamesList: any[];
         readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
         readonly rpcManager: RpcManager;
     } & {
         waitForAssembly(assemblyName: string): Promise<({
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -391,9 +407,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -408,6 +425,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -426,8 +444,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -435,6 +453,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -458,9 +477,10 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -475,6 +495,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -493,21 +514,15 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: {
-            stopToken?: string;
-            sessionId: string;
-        }): Promise<{
+        }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: {
-            stopToken?: string;
-            sessionId: string;
-        }): Promise<{
+        }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         isValidRefName(refName: string, assemblyName: string): boolean;
@@ -515,7 +530,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         afterAttach(): void;
         removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
         addAssembly(configuration: any): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     rpcManager: RpcManager;
     adminMode: boolean;
@@ -528,7 +543,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
     setDefaultSession(): void;
     setSessionPath(path: string): void;
     renameCurrentSession(newName: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
 export type BaseRootModel = Instance<BaseRootModelType>;
 export declare function isRootModel(thing: unknown): thing is BaseRootModelType;

package/esm/RootModel/BaseRootModel.js

@@ -1,7 +1,7 @@
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyManagerFactory from '@jbrowse/core/assemblyManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { cast, getSnapshot, isStateTreeNode, types } from 'mobx-state-tree';
+import { cast, getSnapshot, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }) {
     return types
         .model('BaseRootModel', {

package/esm/RootModel/FormatAbout.d.ts

@@ -1,4 +1,4 @@
-export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export declare function FormatAboutConfigSchemaFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     config: {
         type: string;
         description: string;
@@ -9,4 +9,4 @@ export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/
         type: string;
         defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/FormatDetails.d.ts

@@ -1,4 +1,4 @@
-export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export declare function FormatDetailsConfigSchemaFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     feature: {
         type: string;
         description: string;
@@ -21,4 +21,4 @@ export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/cor
         defaultValue: number;
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -1,5 +1,5 @@
-export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export declare function HierarchicalConfigSchemaFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    sort: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         trackNames: {
             type: string;
             defaultValue: boolean;
@@ -8,8 +8,8 @@ export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    defaultCollapsed: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         categoryNames: {
             type: string;
             defaultValue: never[];
@@ -22,5 +22,5 @@ export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/InternetAccounts.d.ts

@@ -1,15 +1,15 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { UriLocation } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
-export declare function InternetAccountsRootModelMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export declare function InternetAccountsRootModelMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
 }, {
     initializeInternetAccount(internetAccountConfig: AnyConfigurationModel, initialSnapshot?: {}): any;
     createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
     findAppropriateInternetAccount(location: UriLocation): any;
 } & {
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type RootModelWithInternetAccountsType = ReturnType<typeof InternetAccountsRootModelMixin>;
 export type RootModelWithInternetAccounts = Instance<RootModelWithInternetAccountsType>;

package/esm/RootModel/InternetAccounts.js

@@ -1,5 +1,5 @@
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, types } from 'mobx-state-tree';
 export function InternetAccountsRootModelMixin(pluginManager) {
     return types
         .model({
@@ -65,12 +65,12 @@ export function InternetAccountsRootModelMixin(pluginManager) {
     }))
         .actions(self => ({
         afterCreate() {
-            addDisposer(self, autorun(() => {
+            addDisposer(self, autorun(function internetAccountsAutorun() {
                 const { jbrowse } = self;
                 for (const internetAccount of jbrowse.internetAccounts) {
                     self.initializeInternetAccount(internetAccount);
                 }
-            }));
+            }, { name: 'InternetAccounts' }));
         },
     }));
 }

package/esm/RootModel/index.d.ts

@@ -1,5 +1,5 @@
-export * from './BaseRootModel';
-export * from './InternetAccounts';
-export * from './FormatAbout';
-export * from './FormatDetails';
-export * from './HierarchicalConfig';
+export * from './BaseRootModel.ts';
+export * from './InternetAccounts.ts';
+export * from './FormatAbout.ts';
+export * from './FormatDetails.ts';
+export * from './HierarchicalConfig.ts';

package/esm/RootModel/index.js

@@ -1,5 +1,5 @@
-export * from './BaseRootModel';
-export * from './InternetAccounts';
-export * from './FormatAbout';
-export * from './FormatDetails';
-export * from './HierarchicalConfig';
+export * from "./BaseRootModel.js";
+export * from "./InternetAccounts.js";
+export * from "./FormatAbout.js";
+export * from "./FormatDetails.js";
+export * from "./HierarchicalConfig.js";

package/esm/Session/BaseSession.d.ts

@@ -1,17 +1,17 @@
-import type { BaseRootModelType } from '../RootModel/BaseRootModel';
+import type { BaseRootModelType } from '../RootModel/BaseRootModel.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    margin: import("mobx-state-tree").IType<number | undefined, number, number>;
+import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
+export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
 }, {
     selection: unknown;
     hovered: unknown;
 } & {
-    readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
+    readonly root: import("@jbrowse/mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -24,7 +24,11 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     setSelection(thing: unknown): void;
     clearSelection(): void;
     setHovered(thing: unknown): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+}>>;
 export type BaseSessionType = ReturnType<typeof BaseSessionModel>;
 export type BaseSession = Instance<BaseSessionType>;
 export declare function isBaseSession(thing: IAnyStateTreeNode): thing is BaseSession;

package/esm/Session/BaseSession.js

@@ -1,5 +1,5 @@
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { getParent, isStateTreeNode, types } from 'mobx-state-tree';
+import { getParent, isStateTreeNode, types } from '@jbrowse/mobx-state-tree';
 export function BaseSessionModel(_pluginManager) {
     return types
         .model({
@@ -48,7 +48,17 @@ export function BaseSessionModel(_pluginManager) {
         setHovered(thing) {
             self.hovered = thing;
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { margin, ...rest } = snap;
+        return {
+            ...rest,
+            ...(margin ? { margin } : {}),
+        };
+    });
 }
 export function isBaseSession(thing) {
     return 'id' in thing && 'name' in thing && 'root' in thing;