@jbrowse/product-core 3.6.5 → 4.0.0

package/esm/Session/SessionTracks.d.ts

@@ -1,12 +1,12 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function SessionTracksManagerSessionMixin(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 SessionTracksManagerSessionMixin(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>;
 } & {
-    sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
 }, {
     selection: unknown;
     hovered: unknown;
@@ -16,8 +16,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
@@ -25,6 +25,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -48,8 +49,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -64,6 +67,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -82,8 +86,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -91,6 +95,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -114,8 +119,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -130,6 +137,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -148,17 +156,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -182,8 +191,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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 +209,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -216,8 +228,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -225,6 +237,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -248,8 +261,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -264,6 +279,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -282,18 +298,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -317,8 +335,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -333,6 +353,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -351,8 +372,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -360,6 +381,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -383,8 +405,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -399,6 +423,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -417,20 +442,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -454,8 +480,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -470,6 +498,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -488,8 +517,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -497,6 +526,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -520,8 +550,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -536,6 +568,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -554,21 +587,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -576,9 +603,9 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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;
@@ -586,6 +613,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -609,8 +637,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -625,6 +655,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -643,17 +674,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -677,8 +709,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -693,6 +727,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -711,8 +746,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -720,6 +755,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -743,8 +779,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -759,6 +797,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -777,18 +816,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -812,8 +853,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -828,6 +871,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -846,8 +890,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -855,6 +899,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -878,8 +923,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -894,6 +941,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -912,20 +960,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -949,8 +998,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -965,6 +1016,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -983,8 +1035,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -992,6 +1044,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1015,8 +1068,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1031,6 +1086,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1049,21 +1105,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1071,8 +1121,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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("mobx-state-tree/dist/internal").NonEmptyObject & {
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
         error: unknown;
@@ -1080,17 +1130,17 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         pluginManager: PluginManager;
     } & {
         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;
-    } & 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;
@@ -1098,6 +1148,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1121,8 +1172,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1137,6 +1190,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1155,17 +1209,18 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1189,8 +1244,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1205,6 +1262,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1223,8 +1281,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1232,6 +1290,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1255,8 +1314,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1271,6 +1332,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1289,18 +1351,20 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1324,8 +1388,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1340,6 +1406,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1358,8 +1425,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1367,6 +1434,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1390,8 +1458,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1406,6 +1476,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1424,20 +1495,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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: 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;
@@ -1461,8 +1533,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1477,6 +1551,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1495,8 +1570,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1504,6 +1579,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -1527,8 +1603,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 readonly refNames: string[] | undefined;
             } & {
                 getCanonicalRefName(refName: string): string | undefined;
+                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[];
@@ -1543,6 +1621,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
@@ -1561,21 +1640,15 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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;
@@ -1583,7 +1656,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             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: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
@@ -1592,25 +1665,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         pluginManager: PluginManager;
     } & {
         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;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     readonly configuration: {
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
 } & {
@@ -1620,11 +1689,17 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     clearSelection(): void;
     setHovered(thing: unknown): void;
 } & {
-    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
+    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement.ts").ReferringNode[];
 } & {
-    removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
+    removeReferring(referring: import("./ReferenceManagement.ts").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
 } & {
     readonly tracks: AnyConfigurationModel[];
+    readonly assemblies: {
+        sequence: {
+            trackId: string;
+        };
+    }[];
+    readonly tracksById: Record<string, AnyConfigurationModel>;
 } & {
     addTrackConf(trackConf: AnyConfiguration): any;
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
@@ -1633,7 +1708,13 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     addTrackConf(trackConf: AnyConfiguration): any;
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
-}, 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>;
+} & {
+    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+}>>;
 export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;
 export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>;
 export declare function isSessionWithSessionTracks(thing: IAnyStateTreeNode): thing is SessionWithSessionTracks;