@jbrowse/react-app2 3.7.0 → 4.0.1

package/esm/createViewState.d.ts

@@ -1,6 +1,6 @@
-import type { Config } from './types';
+import type { Config } from './types.ts';
 import type { PluginConstructor } from '@jbrowse/core/Plugin';
-import type { IJsonPatch } from 'mobx-state-tree';
+import type { IJsonPatch } from '@jbrowse/mobx-state-tree';
 export default function createViewState(opts: {
     config: Config;
     plugins?: PluginConstructor[];
@@ -11,8 +11,8 @@ export default function createViewState(opts: {
     session: any;
     sessionPath: string;
     assemblyManager: {
-        assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+        assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -20,6 +20,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -43,9 +44,10 @@ export default function createViewState(opts: {
             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[];
@@ -60,6 +62,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -78,8 +81,8 @@ export default function createViewState(opts: {
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -87,6 +90,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -110,9 +114,10 @@ export default function createViewState(opts: {
             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[];
@@ -127,6 +132,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -145,17 +151,18 @@ export default function createViewState(opts: {
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         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;
@@ -179,9 +186,10 @@ export default function createViewState(opts: {
             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[];
@@ -196,6 +204,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -214,8 +223,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -223,6 +232,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -246,9 +256,10 @@ export default function createViewState(opts: {
             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[];
@@ -263,6 +274,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -281,19 +293,20 @@ export default function createViewState(opts: {
                 [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;
@@ -317,9 +330,10 @@ export default function createViewState(opts: {
             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[];
@@ -334,6 +348,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -352,8 +367,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -361,6 +376,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -384,9 +400,10 @@ export default function createViewState(opts: {
             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[];
@@ -401,6 +418,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -419,20 +437,21 @@ export default function createViewState(opts: {
                 [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: import("@jbrowse/core/rpc/RpcManager").default;
     } & {
         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;
@@ -456,9 +475,10 @@ export default function createViewState(opts: {
             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[];
@@ -473,6 +493,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -491,8 +512,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -500,6 +521,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -523,9 +545,10 @@ export default function createViewState(opts: {
             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[];
@@ -540,6 +563,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -558,21 +582,15 @@ export default function createViewState(opts: {
                 [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.ts").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.ts").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         isValidRefName(refName: string, assemblyName: string): boolean;
@@ -580,9 +598,9 @@ export default function createViewState(opts: {
         afterAttach(): void;
         removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
         addAssembly(configuration: any): void;
-    } & import("mobx-state-tree").IStateTreeNode<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<import("mobx-state-tree").IAnyType>>;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -590,6 +608,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -613,9 +632,10 @@ export default function createViewState(opts: {
             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[];
@@ -630,6 +650,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -648,17 +669,18 @@ export default function createViewState(opts: {
                 [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;
@@ -682,9 +704,10 @@ export default function createViewState(opts: {
             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[];
@@ -699,6 +722,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -717,8 +741,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -726,6 +750,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -749,9 +774,10 @@ export default function createViewState(opts: {
             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[];
@@ -766,6 +792,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -784,19 +811,20 @@ export default function createViewState(opts: {
                 [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;
@@ -820,9 +848,10 @@ export default function createViewState(opts: {
             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[];
@@ -837,6 +866,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -855,8 +885,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -864,6 +894,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -887,9 +918,10 @@ export default function createViewState(opts: {
             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[];
@@ -904,6 +936,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -922,20 +955,21 @@ export default function createViewState(opts: {
                 [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: import("@jbrowse/core/rpc/RpcManager").default;
     } & {
         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;
@@ -959,9 +993,10 @@ export default function createViewState(opts: {
             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[];
@@ -976,6 +1011,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -994,8 +1030,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -1003,6 +1039,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -1026,9 +1063,10 @@ export default function createViewState(opts: {
             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[];
@@ -1043,6 +1081,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1061,21 +1100,15 @@ export default function createViewState(opts: {
                 [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.ts").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.ts").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1083,9 +1116,9 @@ export default function createViewState(opts: {
         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]>>;
-    internetAccounts: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
-} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IAnyType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     adminMode: boolean;
     error: unknown;
@@ -1093,7 +1126,7 @@ export default function createViewState(opts: {
     pluginManager: import("@jbrowse/core/PluginManager").default;
 } & {
     setError(error: unknown): void;
-    setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
+    setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
     setDefaultSession(): void;
     setSessionPath(path: string): void;
     renameCurrentSession(newName: string): void;
@@ -1121,20 +1154,20 @@ export default function createViewState(opts: {
     error: unknown;
 } & {
     afterCreate(): void;
-    setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
+    setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
     setPluginsUpdated(flag: boolean): void;
     setDefaultSession(): void;
     renameCurrentSession(sessionName: string): void;
     setError(error?: unknown): void;
 } & {
     menus(): import("@jbrowse/app-core").Menu[];
-} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-    jbrowse: import("mobx-state-tree").IAnyType;
-    session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").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<import("mobx-state-tree").IAnyType>>;
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+    jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+    session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -1142,6 +1175,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -1165,9 +1199,10 @@ export default function createViewState(opts: {
             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[];
@@ -1182,6 +1217,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1200,17 +1236,18 @@ export default function createViewState(opts: {
                 [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;
@@ -1234,9 +1271,10 @@ export default function createViewState(opts: {
             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[];
@@ -1251,6 +1289,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1269,8 +1308,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -1278,6 +1317,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -1301,9 +1341,10 @@ export default function createViewState(opts: {
             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[];
@@ -1318,6 +1359,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1336,19 +1378,20 @@ export default function createViewState(opts: {
                 [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;
@@ -1372,9 +1415,10 @@ export default function createViewState(opts: {
             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[];
@@ -1389,6 +1433,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1407,8 +1452,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -1416,6 +1461,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -1439,9 +1485,10 @@ export default function createViewState(opts: {
             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[];
@@ -1456,6 +1503,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1474,20 +1522,21 @@ export default function createViewState(opts: {
                 [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: import("@jbrowse/core/rpc/RpcManager").default;
     } & {
         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;
@@ -1511,9 +1560,10 @@ export default function createViewState(opts: {
             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[];
@@ -1528,6 +1578,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1546,8 +1597,8 @@ export default function createViewState(opts: {
                 [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -1555,6 +1606,7 @@ export default function createViewState(opts: {
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -1578,9 +1630,10 @@ export default function createViewState(opts: {
             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[];
@@ -1595,6 +1648,7 @@ export default function createViewState(opts: {
                 [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>;
@@ -1613,21 +1667,15 @@ export default function createViewState(opts: {
                 [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.ts").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.ts").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1635,9 +1683,9 @@ export default function createViewState(opts: {
         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]>;
 } & {
-    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
 }, {
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     adminMode: boolean;
@@ -1646,7 +1694,7 @@ export default function createViewState(opts: {
     pluginManager: import("@jbrowse/core/PluginManager").default;
 } & {
     setError(error: unknown): void;
-    setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
+    setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
     setDefaultSession(): void;
     setSessionPath(path: string): void;
     renameCurrentSession(newName: string): void;
@@ -1674,11 +1722,11 @@ export default function createViewState(opts: {
     error: unknown;
 } & {
     afterCreate(): void;
-    setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
+    setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
     setPluginsUpdated(flag: boolean): void;
     setDefaultSession(): void;
     renameCurrentSession(sessionName: string): void;
     setError(error?: unknown): void;
 } & {
     menus(): import("@jbrowse/app-core").Menu[];
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;